Sun Jan 7 01:10:08 UTC 2024 I: starting to build gromacs/bullseye/amd64 on jenkins on '2024-01-07 01:09' Sun Jan 7 01:10:08 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_22/12086/console.log Sun Jan 7 01:10:08 UTC 2024 I: Downloading source for bullseye/gromacs=2020.6-2 --2024-01-07 01:10:09-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/gromacs/gromacs_2020.6-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2948 (2.9K) [text/prs.lines.tag] Saving to: ‘gromacs_2020.6-2.dsc’ 0K .. 100% 198M=0s 2024-01-07 01:10:09 (198 MB/s) - ‘gromacs_2020.6-2.dsc’ saved [2948/2948] Sun Jan 7 01:10:09 UTC 2024 I: gromacs_2020.6-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: gromacs Binary: gromacs, gromacs-data, libgromacs5, libgromacs-dev, gromacs-mpich, gromacs-openmpi Architecture: any all Version: 2020.6-2 Maintainer: Debichem Team Uploaders: Nicholas Breen Homepage: http://www.gromacs.org/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, perl Build-Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.4-5), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev Build-Depends-Indep: doxygen, ghostscript, graphviz, imagemagick, mscgen, python3-sphinx, rdfind, symlinks, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra Package-List: gromacs deb science optional arch=any gromacs-data deb science optional arch=all gromacs-mpich deb science optional arch=any gromacs-openmpi deb science optional arch=any libgromacs-dev deb libdevel optional arch=any libgromacs5 deb libs optional arch=any Checksums-Sha1: 680a608945f3aec194909fb46259510e1f9f4b13 48541232 gromacs_2020.6.orig-regressiontests.tar.gz 756a4fb4168b55a59fa6ff49ad696a374a1a530b 29196621 gromacs_2020.6.orig.tar.gz 2988a7a45f8776e0d5b44f4fa7eb01a27d95c35a 38316 gromacs_2020.6-2.debian.tar.xz Checksums-Sha256: efefa9ad818f39bdf9eff9c3c7051ea384a1a2fa6a6665c610010bb8ac0bafdd 48541232 gromacs_2020.6.orig-regressiontests.tar.gz d8bbe57ed3c9925a8cb99ecfe39e217f930bed47d5268a9e42b33da544bdb2ee 29196621 gromacs_2020.6.orig.tar.gz e81365917428f105e9929e8ebbedcb93f9a66c90818fbdadf8480b9b44e4feec 38316 gromacs_2020.6-2.debian.tar.xz Files: a76f7d8605b276e11f7e11d0906636ba 48541232 gromacs_2020.6.orig-regressiontests.tar.gz dc0156d330ae94bb53d75f419229aec8 29196621 gromacs_2020.6.orig.tar.gz d637708cd893d9169dcfb9345f978ef7 38316 gromacs_2020.6-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCAAwFiEEhD5fph5gYziYdtLl7kr9aexlEI8FAmBhZDkSHG5icmVlbkBk ZWJpYW4ub3JnAAoJEO5K/WnsZRCP4WYP/1bgqtcztpNQ0+Hd9JjymcOUmdPl9v8I N7dILSos2Ph6PeB5lYoVc22cvqThbPGbK3kO50lCFf3vr+4jA5Urjrv6EfJK5uCc AjQqsqh0YvwjBJU16WHpri5txTK0kXIyPB+QUqN36hzfEvS+1Sax3azaW723UEpv elIKqrpSAeEDOX+NynDlqC1Q+Igzz0/OkUxwnDG7avpXM4pUwhrUSrSwd0fIBoFD OBPwXeiO3UiCMpMhKNjLIcCg+39vWQVp28TlmgeaT0X94w9Gxlt1ANaOJ9TPz9Ak vm9n3W2nsewwrGiAjI5uUc4XWkdVvbPiZAo56mNhu3WAeUL/iqH0NDPHB60lrhA2 0LN1ufS5RxWOFYugMhLmSn00NoSpJp3dPWOFlIYz00niD0BKAhkrC62L+C2zl1Jr J9Q2UnyUcebFR3yJzdSgGJqLvV3Ui5KeEVkHmoCL8QUOe8tvdqzjbARqpU0u53Y9 wBBYXcEIV/IqP33vT2yaj1GZAPzhpUVSgeTg3+CspN8DEKu3ZpXTrOPVUqosaY2D SadQJijjQ4oJ6auk6/thbFcQn/cWs+HQBAMzNDu/z3B3QwPZc8mRoY1VEMJZ55P9 +dkzoyaDY9pgBYbw8aCnfIOccdXdOpCn3iuhkhyBNclAXFV5wwH3m8s9YAm/wKS0 2KnD2THHTdXM =3tPa -----END PGP SIGNATURE----- Sun Jan 7 01:10:09 UTC 2024 I: Checking whether the package is not for us Sun Jan 7 01:10:09 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Sun Jan 7 01:10:09 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Sun Jan 7 03:25:46 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 7 19:33:17 -12 2025 I: pbuilder-time-stamp: 1738999997 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gromacs_2020.6-2.dsc] I: copying [./gromacs_2020.6.orig-regressiontests.tar.gz] I: copying [./gromacs_2020.6.orig.tar.gz] I: copying [./gromacs_2020.6-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.IV_tZh3q/trustedkeys.kbx': General error gpgv: Signature made Mon Mar 29 05:23:05 2021 gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F gpgv: issuer "nbreen@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gromacs_2020.6-2.dsc dpkg-source: info: extracting gromacs in gromacs-2020.6 dpkg-source: info: unpacking gromacs_2020.6.orig.tar.gz dpkg-source: info: unpacking gromacs_2020.6.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2020.6-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-listed-forces-test.patch dpkg-source: info: applying arm64-disable-numa-test.patch dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3709870/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='9409e1b3684e42e48aa412548191310f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3709870' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.C1oULqzK/pbuilderrc_u59Y --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.C1oULqzK/b1 --logfile b1/build.log gromacs_2020.6-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 7 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 8 15:46 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3709870/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.4-5), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev, doxygen, ghostscript, graphviz, imagemagick, mscgen, python3-sphinx, rdfind, symlinks, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17743 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libmpich-dev (>= 3.4-5); however: Package libmpich-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev (>= 1.10.2-7); however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libx11-dev; however: Package libx11-dev is not installed. pbuilder-satisfydepends-dummy depends on lsb-release; however: Package lsb-release is not installed. pbuilder-satisfydepends-dummy depends on mpich; however: Package mpich is not installed. pbuilder-satisfydepends-dummy depends on openmpi-bin; however: Package openmpi-bin is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on mscgen; however: Package mscgen is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. pbuilder-satisfydepends-dummy depends on symlinks; however: Package symlinks is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} distro-info-data{a} docutils-common{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} gettext{a} gettext-base{a} gfortran{a} gfortran-10{a} ghostscript{a} graphviz{a} groff-base{a} hicolor-icon-theme{a} hwloc-nox{a} ibverbs-providers{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libann0{a} libaom0{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcbor0{a} libcdt5{a} libcgraph6{a} libclang-cpp11{a} libclang1-11{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2{a} libcurl4{a} libdatrie1{a} libdav1d4{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgd3{a} libgfortran-10-dev{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgs9{a} libgs9-common{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu67{a} libidn11{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp24{a} libkpathsea6{a} liblab-gamut1{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libllvm11{a} liblqr-1-0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmagickcore-6.q16-6{a} libmagickwand-6.q16-6{a} libmd0{a} libmpdec3{a} libmpich-dev{a} libmpich12{a} libncurses6{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenjp2-7{a} libopenmpi-dev{a} libopenmpi3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpciaccess0{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpmix-dev{a} libpmix2{a} libpng16-16{a} libprocps8{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} libptexenc1{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} librdmacm1{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libslurm36{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53{a} libtexluajit2{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libucx0{a} libuv1{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx265-192{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxnvctrl0{a} libxpm4{a} libxrender1{a} libxt6{a} libz3-4{a} libzzip-0-13{a} lsb-release{a} m4{a} man-db{a} media-types{a} mpich{a} mscgen{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-pyparsing{a} python3-requests{a} python3-roman{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-tz{a} python3-urllib3{a} python3.9{a} python3.9-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} symlinks{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} x11-common{a} x11proto-dev{a} xdg-utils{a} xml-core{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus dvisvgm fonts-droid-fallback fonts-liberation gsfonts javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libfile-mimeinfo-perl libglib2.0-data libgpm2 libgts-bin libldap-common libmagickcore-6.q16-6-extra libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lmodern lynx netpbm psmisc publicsuffix python3-pil ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xauth xdg-user-dirs 0 packages upgraded, 281 newly installed, 0 to remove and 0 not upgraded. Need to get 254 MB of archives. After unpacking 1115 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libfftw3-double3 amd64 3.3.8-2 [733 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 fonts-urw-base35 all 20200910-1 [6367 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libaom0 amd64 1.0.0.errata1-3+deb11u1 [1120 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdav1d4 amd64 0.7.1-3 [333 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libde265-0 amd64 1.0.11-0+deb11u1 [179 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libx265-192 amd64 3.4-2 [1095 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libheif1 amd64 1.11.0-1 [191 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 liblqr-1-0 amd64 0.4.2-2.1 [29.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libltdl7 amd64 2.4.6-15 [391 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libopenjp2-7 amd64 2.4.0-3 [172 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u4 [290 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libwebpdemux2 amd64 0.6.1-2.1+deb11u2 [87.8 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libwebpmux3 amd64 0.6.1-2.1+deb11u2 [97.7 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u1 [311 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u1 [772 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 imagemagick-6-common all 8:6.9.11.60+dfsg-1.3+deb11u1 [211 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libmagickcore-6.q16-6 amd64 8:6.9.11.60+dfsg-1.3+deb11u1 [1812 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libmagickwand-6.q16-6 amd64 8:6.9.11.60+dfsg-1.3+deb11u1 [453 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 poppler-data all 0.4.10-1 [1602 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 tzdata all 2021a-1+deb11u10 [286 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 sgml-base all 1.30 [15.1 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 tex-common all 6.16 [53.7 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libcbor0 amd64 0.5.0+dfsg-2 [24.0 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libfido2-1 amd64 1.6.0-2 [53.3 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 openssh-client amd64 1:8.4p1-5+deb11u2 [930 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+deb11u1 [343 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u9 [347 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 distro-info-data all 0.51+deb11u4 [8048 B] Get: 110 http://deb.debian.org/debian bullseye/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 docutils-common all 0.16+dfsg-4 [129 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libclang-cpp11 amd64 1:11.0.1-2 [9632 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libclang1-11 amd64 1:11.0.1-2 [5521 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 doxygen amd64 1.9.1-1 [4232 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 fonts-lmodern all 2.004.5-6.1 [4540 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libgfortran-10-dev amd64 10.2.1-6 [769 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 gfortran-10 amd64 10.2.1-6 [9447 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 gfortran amd64 4:10.2.1-1 [1428 B] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libgs9-common all 9.53.3~dfsg-7+deb11u6 [735 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5+deb11u2 [124 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5+deb11u2 [58.7 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.28-0+deb11u1 [223 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5+deb11u2 [62.6 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libcups2 amd64 2.3.3op2-3+deb11u6 [351 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libidn11 amd64 1.33-3 [116 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libijs-0.35 amd64 0.35-15 [16.4 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libjbig2dec0 amd64 0.19-2 [67.2 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 libgs9 amd64 9.53.3~dfsg-7+deb11u6 [2245 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 ghostscript amd64 9.53.3~dfsg-7+deb11u6 [98.3 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libann0 amd64 1.1.2+doc-7 [25.3 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libcdt5 amd64 2.42.2-5 [62.2 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libcgraph6 amd64 2.42.2-5 [85.5 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 libxpm4 amd64 1:3.5.12-1.1~deb11u1 [49.6 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 libgd3 amd64 2.3.0-2 [137 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4+b1 [158 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 libpathplan4 amd64 2.42.2-5 [64.3 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 libgvc6 amd64 2.42.2-5 [695 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 libgvpr2 amd64 2.42.2-5 [212 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 liblab-gamut1 amd64 2.42.2-5 [221 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 libxaw7 amd64 2:1.0.13-1.1 [202 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 graphviz amd64 2.42.2-5 [632 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 libhwloc15 amd64 2.4.1+dfsg-1 [150 kB] Get: 168 http://deb.debian.org/debian bullseye/main amd64 hwloc-nox amd64 2.4.1+dfsg-1 [190 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 libibverbs1 amd64 33.2-1 [59.4 kB] Get: 172 http://deb.debian.org/debian bullseye/main amd64 ibverbs-providers amd64 33.2-1 [253 kB] Get: 173 http://deb.debian.org/debian bullseye/main amd64 imagemagick-6.q16 amd64 8:6.9.11.60+dfsg-1.3+deb11u1 [383 kB] Get: 174 http://deb.debian.org/debian bullseye/main amd64 imagemagick amd64 8:6.9.11.60+dfsg-1.3+deb11u1 [166 kB] Get: 175 http://deb.debian.org/debian bullseye/main amd64 libapache-pom-java all 18-1 [4676 B] Get: 176 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get: 177 http://deb.debian.org/debian bullseye/main amd64 libblas-dev amd64 3.9.0-3+deb11u1 [161 kB] Get: 178 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 179 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 180 http://deb.debian.org/debian bullseye/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get: 181 http://deb.debian.org/debian bullseye/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 182 http://deb.debian.org/debian bullseye/main amd64 libevent-2.1-7 amd64 2.1.12-stable-1 [188 kB] Get: 183 http://deb.debian.org/debian bullseye/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get: 184 http://deb.debian.org/debian bullseye/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-1 [110 kB] Get: 185 http://deb.debian.org/debian bullseye/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get: 186 http://deb.debian.org/debian bullseye/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-1 [64.1 kB] Get: 187 http://deb.debian.org/debian bullseye/main amd64 libevent-dev amd64 2.1.12-stable-1 [311 kB] Get: 188 http://deb.debian.org/debian bullseye/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.1 [169 kB] Get: 189 http://deb.debian.org/debian bullseye/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get: 190 http://deb.debian.org/debian bullseye/main amd64 librdmacm1 amd64 33.2-1 [68.9 kB] Get: 191 http://deb.debian.org/debian bullseye/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get: 192 http://deb.debian.org/debian bullseye/main amd64 libfftw3-long3 amd64 3.3.8-2 [319 kB] Get: 193 http://deb.debian.org/debian bullseye/main amd64 libfftw3-quad3 amd64 3.3.8-2 [558 kB] Get: 194 http://deb.debian.org/debian bullseye/main amd64 libfftw3-single3 amd64 3.3.8-2 [762 kB] Get: 195 http://deb.debian.org/debian bullseye/main amd64 libfftw3-bin amd64 3.3.8-2 [50.7 kB] Get: 196 http://deb.debian.org/debian bullseye/main amd64 libfftw3-dev amd64 3.3.8-2 [2106 kB] Get: 197 http://deb.debian.org/debian bullseye/main amd64 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 198 http://deb.debian.org/debian bullseye/main amd64 libnuma-dev amd64 2.0.12-1+b1 [39.3 kB] Get: 199 http://deb.debian.org/debian bullseye/main amd64 libltdl-dev amd64 2.4.6-15 [162 kB] Get: 200 http://deb.debian.org/debian bullseye/main amd64 libhwloc-dev amd64 2.4.1+dfsg-1 [231 kB] Get: 201 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get: 202 http://deb.debian.org/debian bullseye/main amd64 libxnvctrl0 amd64 470.141.03-1~deb11u1 [27.5 kB] Get: 203 http://deb.debian.org/debian bullseye/main amd64 ocl-icd-libopencl1 amd64 2.2.14-2 [42.5 kB] Get: 204 http://deb.debian.org/debian bullseye/main amd64 libhwloc-plugins amd64 2.4.1+dfsg-1 [21.4 kB] Get: 205 http://deb.debian.org/debian bullseye/main amd64 libnl-3-dev amd64 3.4.0-1+b1 [102 kB] Get: 206 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-dev amd64 3.4.0-1+b1 [176 kB] Get: 207 http://deb.debian.org/debian bullseye/main amd64 libibverbs-dev amd64 33.2-1 [487 kB] Get: 208 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 209 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 210 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 211 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 212 http://deb.debian.org/debian bullseye/main amd64 libkpathsea6 amd64 2020.20200327.54578-7+deb11u1 [172 kB] Get: 213 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get: 214 http://deb.debian.org/debian bullseye/main amd64 liblapack-dev amd64 3.9.0-3+deb11u1 [4246 kB] Get: 215 http://deb.debian.org/debian bullseye/main amd64 libmpich12 amd64 3.4.1-5~deb11u1 [1987 kB] Get: 216 http://deb.debian.org/debian bullseye/main amd64 libslurm36 amd64 20.11.7+really20.11.4-2+deb11u1 [667 kB] Get: 217 http://deb.debian.org/debian bullseye/main amd64 mpich amd64 3.4.1-5~deb11u1 [219 kB] Get: 218 http://deb.debian.org/debian bullseye/main amd64 libmpich-dev amd64 3.4.1-5~deb11u1 [2343 kB] Get: 219 http://deb.debian.org/debian bullseye/main amd64 libpmix2 amd64 4.0.0-4.1 [552 kB] Get: 220 http://deb.debian.org/debian bullseye/main amd64 libucx0 amd64 1.10.1~rc1+really.1.10.0-1 [649 kB] Get: 221 http://deb.debian.org/debian bullseye/main amd64 libopenmpi3 amd64 4.1.0-10 [2370 kB] Get: 222 http://deb.debian.org/debian bullseye/main amd64 openmpi-common all 4.1.0-10 [179 kB] Get: 223 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 224 http://deb.debian.org/debian bullseye/main amd64 libpmix-dev amd64 4.0.0-4.1 [655 kB] Get: 225 http://deb.debian.org/debian bullseye/main amd64 openmpi-bin amd64 4.1.0-10 [238 kB] Get: 226 http://deb.debian.org/debian bullseye/main amd64 libopenmpi-dev amd64 4.1.0-10 [1192 kB] Get: 227 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get: 228 http://deb.debian.org/debian bullseye/main amd64 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 229 http://deb.debian.org/debian bullseye/main amd64 libptexenc1 amd64 2020.20200327.54578-7+deb11u1 [64.7 kB] Get: 230 http://deb.debian.org/debian bullseye/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 231 http://deb.debian.org/debian bullseye/main amd64 libsynctex2 amd64 2020.20200327.54578-7+deb11u1 [83.4 kB] Get: 232 http://deb.debian.org/debian bullseye/main amd64 libteckit0 amd64 2.5.10+ds1-3 [329 kB] Get: 233 http://deb.debian.org/debian bullseye/main amd64 libtexlua53 amd64 2020.20200327.54578-7+deb11u1 [131 kB] Get: 234 http://deb.debian.org/debian bullseye/main amd64 libtexluajit2 amd64 2020.20200327.54578-7+deb11u1 [267 kB] Get: 235 http://deb.debian.org/debian bullseye/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 236 http://deb.debian.org/debian bullseye/main amd64 x11proto-dev all 2020.1-1 [594 kB] Get: 237 http://deb.debian.org/debian bullseye/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get: 238 http://deb.debian.org/debian bullseye/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get: 239 http://deb.debian.org/debian bullseye/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 240 http://deb.debian.org/debian bullseye/main amd64 libxcb1-dev amd64 1.14-3 [176 kB] Get: 241 http://deb.debian.org/debian bullseye/main amd64 libx11-dev amd64 2:1.7.2-1+deb11u1 [843 kB] Get: 242 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get: 243 http://deb.debian.org/debian bullseye/main amd64 libzzip-0-13 amd64 0.13.62-3.3+deb11u1 [55.9 kB] Get: 244 http://deb.debian.org/debian bullseye/main amd64 lsb-release all 11.1.0 [27.9 kB] Get: 245 http://deb.debian.org/debian bullseye/main amd64 mscgen amd64 0.20-14 [49.5 kB] Get: 246 http://deb.debian.org/debian bullseye/main amd64 preview-latex-style all 12.2-1 [201 kB] Get: 247 http://deb.debian.org/debian bullseye/main amd64 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 248 http://deb.debian.org/debian bullseye/main amd64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 249 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 250 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get: 251 http://deb.debian.org/debian bullseye/main amd64 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 252 http://deb.debian.org/debian bullseye/main amd64 python3-certifi all 2020.6.20-1 [151 kB] Get: 253 http://deb.debian.org/debian bullseye/main amd64 python3-chardet all 4.0.0-1 [99.0 kB] Get: 254 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 255 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 256 http://deb.debian.org/debian bullseye/main amd64 python3-roman all 2.0.0-5 [9064 B] Get: 257 http://deb.debian.org/debian bullseye/main amd64 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 258 http://deb.debian.org/debian bullseye/main amd64 python3-idna all 2.10-1 [37.4 kB] Get: 259 http://deb.debian.org/debian bullseye/main amd64 python3-imagesize all 1.2.0-2 [5824 B] Get: 260 http://deb.debian.org/debian bullseye/main amd64 python3-markupsafe amd64 1.1.1-1+b3 [15.2 kB] Get: 261 http://deb.debian.org/debian bullseye/main amd64 python3-jinja2 all 2.11.3-1 [114 kB] Get: 262 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 263 http://deb.debian.org/debian bullseye/main amd64 python3-packaging all 20.9-2 [33.5 kB] Get: 264 http://deb.debian.org/debian bullseye/main amd64 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 265 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 266 http://deb.debian.org/debian bullseye/main amd64 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 267 http://deb.debian.org/debian bullseye/main amd64 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 268 http://deb.debian.org/debian bullseye/main amd64 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 269 http://deb.debian.org/debian bullseye/main amd64 sphinx-common all 3.4.3-2 [578 kB] Get: 270 http://deb.debian.org/debian bullseye/main amd64 python3-sphinx all 3.4.3-2 [545 kB] Get: 271 http://deb.debian.org/debian bullseye/main amd64 rdfind amd64 1.4.1-1+b3 [40.7 kB] Get: 272 http://deb.debian.org/debian bullseye/main amd64 symlinks amd64 1.4-4 [11.3 kB] Get: 273 http://deb.debian.org/debian bullseye/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 274 http://deb.debian.org/debian bullseye/main amd64 texlive-binaries amd64 2020.20200327.54578-7+deb11u1 [10.1 MB] Get: 275 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 276 http://deb.debian.org/debian bullseye/main amd64 texlive-base all 2020.20210202-3 [20.8 MB] Get: 277 http://deb.debian.org/debian bullseye/main amd64 texlive-fonts-recommended all 2020.20210202-3 [5002 kB] Get: 278 http://deb.debian.org/debian bullseye/main amd64 texlive-latex-base all 2020.20210202-3 [1120 kB] Get: 279 http://deb.debian.org/debian bullseye/main amd64 texlive-latex-recommended all 2020.20210202-3 [14.5 MB] Get: 280 http://deb.debian.org/debian bullseye/main amd64 texlive-pictures all 2020.20210202-3 [6743 kB] Get: 281 http://deb.debian.org/debian bullseye/main amd64 texlive-latex-extra all 2020.20210202-3 [13.7 MB] Fetched 254 MB in 11s (23.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17743 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libfftw3-double3:amd64. Preparing to unpack .../05-libfftw3-double3_3.3.8-2_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.8-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../06-libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../07-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:amd64. 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Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up m4 (1.4.18-5) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnuma-dev:amd64 (2.0.12-1+b1) ... Setting up libnl-route-3-200:amd64 (3.4.0-1+b1) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up libptexenc1:amd64 (2020.20200327.54578-7+deb11u1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libevent-dev (2.1.12-stable-1) ... Setting up liblapack-dev:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up gfortran-10 (10.2.1-6) ... Setting up libclang1-11 (1:11.0.1-2) ... Setting up ucf (3.0043) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libgvpr2:amd64 (2.42.2-5) ... Setting up dwz (0.13+20210201-1) ... Setting up libnl-3-dev:amd64 (3.4.0-1+b1) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u9) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u1) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libfftw3-dev:amd64 (3.3.8-2) ... Setting up libavahi-client3:amd64 (0.8-5+deb11u2) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libibverbs1:amd64 (33.2-1) ... Setting up libxcb1-dev:amd64 (1.14-3) ... Setting up libxpm4:amd64 (1:3.5.12-1.1~deb11u1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up ibverbs-providers:amd64 (33.2-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up mpich (3.4.1-5~deb11u1) ... update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode Setting up openssh-client (1:8.4p1-5+deb11u2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libheif1:amd64 (1.11.0-1) ... Setting up libx11-dev:amd64 (2:1.7.2-1+deb11u1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:10.2.1-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libxnvctrl0:amd64 (470.141.03-1~deb11u1) ... Setting up libclang-cpp11 (1:11.0.1-2) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.16) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Setting up libltdl-dev:amd64 (2.4.6-15) ... Setting up doxygen (1.9.1-1) ... Setting up sphinx-common (3.4.3-2) ... Setting up libmpich-dev:amd64 (3.4.1-5~deb11u1) ... update-alternatives: using /usr/include/x86_64-linux-gnu/mpich to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libcups2:amd64 (2.3.3op2-3+deb11u6) ... Setting up cmake (3.18.4-2+deb11u1) ... Setting up libhwloc-dev:amd64 (2.4.1+dfsg-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up librdmacm1:amd64 (33.2-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libucx0:amd64 (1.10.1~rc1+really.1.10.0-1) ... Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up libgs9:amd64 (9.53.3~dfsg-7+deb11u6) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up preview-latex-style (12.2-1) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libxaw7:amd64 (2:1.0.13-1.1) ... Setting up libibverbs-dev:amd64 (33.2-1) ... Setting up ghostscript (9.53.3~dfsg-7+deb11u6) ... Setting up libhwloc-plugins:amd64 (2.4.1+dfsg-1) ... Setting up python3-markupsafe (1.1.1-1+b3) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-2) ... Setting up libmagickcore-6.q16-6:amd64 (8:6.9.11.60+dfsg-1.3+deb11u1) ... Setting up python3-roman (2.0.0-5) ... Setting up python3-jinja2 (2.11.3-1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.1.0-1) ... Setting up libgd3:amd64 (2.3.0-2) ... Setting up python3-idna (2.10-1) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up texlive-binaries (2020.20200327.54578-7+deb11u1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libmagickwand-6.q16-6:amd64 (8:6.9.11.60+dfsg-1.3+deb11u1) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up lsb-release (11.1.0) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up texlive-base (2020.20210202-3) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:amd64 (4.0.0-4.1) ... Setting up mscgen (0.20-14) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-alabaster (0.7.8-1.1) ... Setting up libopenmpi3:amd64 (4.1.0-10) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-packaging (20.9-2) ... Setting up python3-chardet (4.0.0-1) ... Setting up texlive-latex-base (2020.20210202-3) ... Setting up texlive-latex-recommended (2020.20210202-3) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up libgvc6 (2.42.2-5) ... Setting up texlive-pictures (2020.20210202-3) ... Setting up imagemagick-6.q16 (8:6.9.11.60+dfsg-1.3+deb11u1) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up texlive-fonts-recommended (2020.20210202-3) ... Setting up libpmix-dev:amd64 (4.0.0-4.1) ... Setting up openmpi-bin (4.1.0-10) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up graphviz (2.42.2-5) ... Setting up texlive-latex-extra (2020.20210202-3) ... Setting up imagemagick (8:6.9.11.60+dfsg-1.3+deb11u1) ... Setting up libopenmpi-dev:amd64 (4.1.0-10) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-4) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (3.4.3-2) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.16) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gromacs-2020.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gromacs_2020.6-2_source.changes dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2020.6-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh_testdir dh_testroot rm -rf build docs/doxygen/*.pyc dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \ debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian debian/rules binary dh_testdir (mkdir -p build/basic; cd build/basic; cmake /build/reproducible-path/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "3.4.3", minimum required is "1.6.1") found components: pygments -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.1") found components: doxygen dot -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2020.6/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake /build/reproducible-path/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:217 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "3.4.3", minimum required is "1.6.1") found components: pygments -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.1") found components: doxygen dot -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2020.6/build/basic-dp (mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /build/reproducible-path/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich") -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.mpich - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.mpich" -- Using manually set library suffix: "_mpi.mpich" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2020.6/build/mpich (mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /build/reproducible-path/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich") -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.mpich - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:217 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.mpich" -- Using manually set library suffix: "_mpi_d.mpich" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2020.6/build/mpich-dp (mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /build/reproducible-path/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi") -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.openmpi" -- Using manually set library suffix: "_mpi.openmpi" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2020.6/build/openmpi (mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /build/reproducible-path/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi") -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:217 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.openmpi" -- Using manually set library suffix: "_mpi_d.openmpi" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2020.6/build/openmpi-dp touch configure-stamp dh_testdir /usr/bin/make -j16 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend Scanning dependencies of target scanner make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib Scanning dependencies of target release-version-info make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/parser.cpp /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build Scanning dependencies of target vmddlopen make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target tng_io_obj cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/scanner.cpp /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/vmd_molfile/vmddlopen.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c Scanning dependencies of target linearalgebra Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp Scanning dependencies of target view_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' Scanning dependencies of target thread_mpi make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/view/3dview.cpp Scanning dependencies of target modularsimulator make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c [ 0%] Built target vmddlopen cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/basic/src 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make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/view/manager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 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'/build/reproducible-path/gromacs-2020.6/build/basic' Scanning dependencies of target gmxapi cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/gmx.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/version.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 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/build/reproducible-path/gromacs-2020.6/src/api/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.5.0.0 /usr/lib/x86_64-linux-gnu/libX11.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 98%] Built target template make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 98%] Built target gmx cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../../lib/libgmxapi.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi.so.0.1.0 ../../../lib/libgmxapi.so.0 ../../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [100%] Built target gmxapi make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -j16 -C build/basic-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend Scanning dependencies of target lmfit_objlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs 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VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/lmfit/lmmin.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend Scanning dependencies of target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio 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-Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/parser.cpp /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/scanner.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend Scanning dependencies of target vmddlopen cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target modularsimulator /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/dict.c /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/vmd_molfile/vmddlopen.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/mdrun.cpp Scanning dependencies of target view_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/view/3dview.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp [ 0%] Built target vmddlopen cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops 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/usr/lib/x86_64-linux-gnu/libhwloc.so -ldl -lrt /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.5.0.0 ../../lib/libgromacs_d.so.5 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= Scanning dependencies of target gmx make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/gmx.cpp Scanning dependencies of target gmxapi cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/legacymodules.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/context.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/md.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/session.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/status.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/system.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/version.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.5.0.0 /usr/lib/x86_64-linux-gnu/libX11.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 98%] Built target gmx cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../../lib/libgmxapi_d.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi_d.so.0.1.0 ../../../lib/libgmxapi_d.so.0 ../../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [100%] Built target gmxapi make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -j16 -C build/basic tests make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 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src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 0%] Built target scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 0%] Built target release-version-info [ 0%] Built target lmfit_objlib [ 1%] Built target tng_io_obj /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend [ 3%] Built target thread_mpi [ 4%] Built target linearalgebra make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/external/googletest/googlemock/gtest /build/reproducible-path/gromacs-2020.6/build/basic/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend [ 5%] Built target modularsimulator make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' Scanning dependencies of target gtest /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/src/gtest-all.cc [ 5%] Built target vmddlopen /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend [ 7%] Built target mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 67%] Built target libgromacs /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 68%] Built target gmxapi cd /build/reproducible-path/gromacs-2020.6/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 68%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 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'/build/reproducible-path/gromacs-2020.6/build/basic' [ 69%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake --color= make[4]: Entering directory 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'/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/interactivetest.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem 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-I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/refdata_tests.cpp Scanning dependencies of target utility-test make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/xvgtest_tests.cpp Scanning dependencies of target onlinehelp-test-shared /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/alignedallocator.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/mock_helptopic.cpp Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests/hashedmap.cpp /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/calc_verletbuf.cpp Scanning dependencies of target applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfitting.cpp Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 69%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fft/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/mdmodulenotification.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 69%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/gputest.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/trajectoryreader.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 69%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 69%] Built target domdec-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 69%] Built target fft-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdspan-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/accessor_policy.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 70%] Built target hardware-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 71%] Built target testutils-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 71%] Built target mdrun_test_infrastructure cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 71%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= Scanning dependencies of target pbcutil-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/defaultinitializationallocator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 71%] Built target pbcutil-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/simulationsignal.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 71%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/updategroups.cpp Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/tables/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread Scanning dependencies of target table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/filenameoptionmanager.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 71%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 72%] Built target applied_forces-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= Scanning dependencies of target topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/mutex.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 74%] Built target mdlib-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 74%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/functions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 74%] Built target taskassignment-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/bias.cpp Scanning dependencies of target simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 74%] Built target pull-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/optional.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/base.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 74%] Built target mdspan-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxana-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests/entropy.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 74%] Built target ewald-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp Scanning dependencies of target pdb2gmx3-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 75%] Built target topology-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx2-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/grid.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 75%] Built target awh-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx1-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/uniformintdistribution.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 75%] Built target table-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxpreprocess-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_msd.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/string_view.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 75%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= Scanning dependencies of target correlations-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/uniformrealdistribution.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 76%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 77%] Built target gmxana-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color= Scanning dependencies of target coordinateio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genrestr.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 78%] Built target random-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target energyanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 78%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/tools/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= Scanning dependencies of target tool-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 80%] Built target options-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/confio.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 81%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= Scanning dependencies of target selection-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/topdirs.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 81%] Built target correlations-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-modules-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-tpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/filemd5.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/dispersion_correction.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 83%] Built target utility-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-output-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 84%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-non-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar_util.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 84%] Built target compat-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 84%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-io-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 84%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-coordination-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/periodicactions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 84%] Built target mdrun-tpi-test /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxapi-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/swapcoords.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 84%] Built target mdrun-modules-test /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxapi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/system.cpp [ 85%] Built target simd-test /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp/workflow/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target workflow-details-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 87%] Built target math-test /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp/workflow/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color= Scanning dependencies of target workflow-details-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 87%] Built target workflow-details-mpi-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/runner.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 87%] Built target mdrun-mpi-coordination-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/stopsignaler.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 88%] Built target workflow-details-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/multisim.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 88%] Built target mdrun-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 89%] Built target fileio-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/rerun.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 89%] Built target gmxapi-mpi-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/simple_mdrun.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 90%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 91%] Built target mdrun-io-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/setstarttime.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 92%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 92%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 94%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 95%] Built target mdrun-mpi-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 96%] Built target coordinateio-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/sasa.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 96%] Built target mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 96%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 97%] Built target commandline-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 98%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [100%] Built target selection-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2020.6/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 ) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2020.6/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2020.6/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2020.6/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2020.6/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2020.6/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (9 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (11 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnys 1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (6 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (1 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (0 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (9 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (0 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (9 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (27 ms total) 1: [ PASSED ] 59 tests. 1/54 Test #1: TestUtilsUnitTests .................. Passed 0.07 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (15 ms) 2: [----------] 1 test from MpiSelfTest (15 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (15 ms total) 2: [ PASSED ] 1 test. 2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.04 sec test 3 Start 3: UtilityUnitTests 3: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/UtilityUnitTests.xml" 3: Test timeout computed to be: 30 3: [==========] Running 347 tests from 56 test cases. 3: [----------] Global test environment set-up. 3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.Move 3: [ OK ] AllocatorTest/0.Move (0 ms) 3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/0 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.Move 3: [ OK ] AllocatorTest/1.Move (0 ms) 3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/1 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.Move 3: [ OK ] AllocatorTest/2.Move (0 ms) 3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/2 (1 ms total) 3: 3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.Move 3: [ OK ] AllocatorTest/3.Move (0 ms) 3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/3 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.Move 3: [ OK ] AllocatorTest/4.Move (0 ms) 3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/4 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.Move 3: [ OK ] AllocatorTest/5.Move (0 ms) 3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/5 (0 ms total) 3: 3: [----------] 1 test from AllocatorUntypedTest 3: [ RUN ] AllocatorUntypedTest.Comparison 3: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 3: [----------] 1 test from AllocatorUntypedTest (0 ms total) 3: 3: [----------] 1 test from EmptyArrayRefTest 3: [ RUN ] EmptyArrayRefTest.IsEmpty 3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyArrayRefTest (0 ms total) 3: 3: [----------] 1 test from EmptyConstArrayRefTest 3: [ RUN ] EmptyConstArrayRefTest.IsEmpty 3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (1 ms) 3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/11 (1 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 3: 3: [----------] 2 tests from CStringUtilityTest 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 3: [----------] 2 tests from CStringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from DefaultInitializationAllocator 3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 3: 3: [----------] 4 tests from EnumerationHelpersTest 3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 3: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 3: 3: [----------] 9 tests from FixedCapacityVectorTest 3: [ RUN ] FixedCapacityVectorTest.IsEmpty 3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PushWorks 3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PopWorks 3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ClearWorks 3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.AtThrows 3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 3: [ RUN ] FixedCapacityVectorTest.IteratorWorks 3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 3: 3: [----------] 5 tests from InMemorySerializerTest 3: [ RUN ] InMemorySerializerTest.Roundtrip 3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (1 ms) 3: [ RUN ] InMemorySerializerTest.SizeIsCorrect 3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 3: [----------] 5 tests from InMemorySerializerTest (1 ms total) 3: 3: [----------] 4 tests from KeyValueTreeSerializerTest 3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 3: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 3: 3: [----------] 6 tests from TreeValueTransformTest 3: [ RUN ] TreeValueTransformTest.SimpleTransforms 3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (13 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromString 3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 3: [ RUN ] TreeValueTransformTest.ScopedTransformRules 3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 3: [----------] 6 tests from TreeValueTransformTest (14 ms total) 3: 3: [----------] 1 test from TreeValueTransformErrorTest 3: [ RUN ] TreeValueTransformErrorTest.ConversionError 3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 3: 3: [----------] 7 tests from LoggerTest 3: [ RUN ] LoggerTest.EmptyLoggerWorks 3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToStream 3: [ OK ] LoggerTest.LogsToStream (0 ms) 3: [ RUN ] LoggerTest.LogsToFile 3: [ OK ] LoggerTest.LogsToFile (0 ms) 3: [ RUN ] LoggerTest.LevelFilteringWorks 3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleStreams 3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleFiles 3: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 3: [ RUN ] LoggerTest.LogsToStreamAndFile 3: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 3: [----------] 7 tests from LoggerTest (0 ms total) 3: 3: [----------] 4 tests from MutexBasicTest 3: [ RUN ] MutexBasicTest.CanBeMade 3: [ OK ] MutexBasicTest.CanBeMade (0 ms) 3: [ RUN ] MutexBasicTest.CanBeLocked 3: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeTryLocked 3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 3: [----------] 4 tests from MutexBasicTest (0 ms total) 3: 3: [----------] 3 tests from MutexTaskTest 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (10 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (13 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 3: [----------] 3 tests from MutexTaskTest (23 ms total) 3: 3: [----------] 2 tests from PathTest 3: [ RUN ] PathTest.StripSourcePrefixWorks 3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 3: [ RUN ] PathTest.SearchOperationsWork 3: [ OK ] PathTest.SearchOperationsWork (0 ms) 3: [----------] 2 tests from PathTest (0 ms total) 3: 3: [----------] 2 tests from PhysicalNodeCommunicatorTest 3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 3: 3: [----------] 9 tests from StringUtilityTest 3: [ RUN ] StringUtilityTest.StartsWith 3: [ OK ] StringUtilityTest.StartsWith (0 ms) 3: [ RUN ] StringUtilityTest.EndsWith 3: [ OK ] StringUtilityTest.EndsWith (0 ms) 3: [ RUN ] StringUtilityTest.StripSuffixIfPresent 3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 3: [ RUN ] StringUtilityTest.StripString 3: [ OK ] StringUtilityTest.StripString (0 ms) 3: [ RUN ] StringUtilityTest.SplitString 3: [ OK ] StringUtilityTest.SplitString (0 ms) 3: [ RUN ] StringUtilityTest.SplitDelimitedString 3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 3: [----------] 9 tests from StringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from FormatStringTest 3: [ RUN ] FormatStringTest.HandlesBasicFormatting 3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 3: [ RUN ] FormatStringTest.HandlesLongStrings 3: [ OK ] FormatStringTest.HandlesLongStrings (1 ms) 3: [----------] 2 tests from FormatStringTest (1 ms total) 3: 3: [----------] 1 test from StringFormatterTest 3: [ RUN ] StringFormatterTest.HandlesBasicFormatting 3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 3: [----------] 1 test from StringFormatterTest (0 ms total) 3: 3: [----------] 1 test from formatAndJoinTest 3: [ RUN ] formatAndJoinTest.Works 3: [ OK ] formatAndJoinTest.Works (0 ms) 3: [----------] 1 test from formatAndJoinTest (0 ms total) 3: 3: [----------] 1 test from JoinStringsTest 3: [ RUN ] JoinStringsTest.Works 3: [ OK ] JoinStringsTest.Works (0 ms) 3: [----------] 1 test from JoinStringsTest (0 ms total) 3: 3: [----------] 6 tests from ReplaceAllTest 3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesNoMatches 3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 3: [----------] 6 tests from ReplaceAllTest (0 ms total) 3: 3: [----------] 10 tests from TextLineWrapperTest 3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectly 3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndent 3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 3: [----------] 10 tests from TextLineWrapperTest (0 ms total) 3: 3: [----------] 6 tests from TextWriterTest 3: [ RUN ] TextWriterTest.WritesLines 3: [ OK ] TextWriterTest.WritesLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInParts 3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 3: [ RUN ] TextWriterTest.WritesWrappedLines 3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 3: [ RUN ] TextWriterTest.TracksNewlines 3: [ OK ] TextWriterTest.TracksNewlines (0 ms) 3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 3: [----------] 6 tests from TextWriterTest (0 ms total) 3: 3: [----------] 1 test from TypeTraitsTest 3: [ RUN ] TypeTraitsTest.IsIntegralConstant 3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 3: [----------] 1 test from TypeTraitsTest (0 ms total) 3: 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (1 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total) 3: 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 3: 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (9 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (1 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (7 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (1 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (18 ms total) 3: 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 347 tests from 56 test cases ran. (61 ms total) 3: [ PASSED ] 347 tests. 3/54 Test #3: UtilityUnitTests .................... Passed 0.09 sec test 4 Start 4: UtilityMpiUnitTests 4: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 4: Test timeout computed to be: 30 4: [==========] Running 2 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from PhysicalNodeCommunicatorTest 4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (32 ms) 4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (15 ms) 4: [----------] 2 tests from PhysicalNodeCommunicatorTest (47 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test case ran. (49 ms total) 4: [ PASSED ] 2 tests. 4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.07 sec test 5 Start 5: MdlibUnitTest 5: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdlibUnitTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 187 tests from 13 test cases. 5: [----------] Global test environment set-up. 5: [----------] 1 test from VerletBufferConstraintTest 5: [ RUN ] VerletBufferConstraintTest.EqualMasses 5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 5: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 5: 5: [----------] 2 tests from PrEbinTest 5: [ RUN ] PrEbinTest.HandlesAverages 5: [ OK ] PrEbinTest.HandlesAverages (1 ms) 5: [ RUN ] PrEbinTest.HandlesEmptyAverages 5: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 5: [----------] 2 tests from PrEbinTest (1 ms total) 5: 5: [----------] 4 tests from ShakeTest 5: [ RUN ] ShakeTest.ConstrainsOneBond 5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 5: [----------] 4 tests from ShakeTest (0 ms total) 5: 5: [----------] 1 test from NullSignalTest 5: [ RUN ] NullSignalTest.NullSignallerWorks 5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 5: [----------] 1 test from NullSignalTest (0 ms total) 5: 5: [----------] 7 tests from SignalTest 5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 5: [----------] 7 tests from SignalTest (0 ms total) 5: 5: [----------] 9 tests from UpdateGroups 5: [ RUN ] UpdateGroups.ethaneUA 5: [ OK ] UpdateGroups.ethaneUA (0 ms) 5: [ RUN ] UpdateGroups.methane 5: [ OK ] UpdateGroups.methane (0 ms) 5: [ RUN ] UpdateGroups.ethane 5: [ OK ] UpdateGroups.ethane (0 ms) 5: [ RUN ] UpdateGroups.butaneUA 5: [ OK ] UpdateGroups.butaneUA (0 ms) 5: [ RUN ] UpdateGroups.waterThreeSite 5: [ OK ] UpdateGroups.waterThreeSite (0 ms) 5: [ RUN ] UpdateGroups.waterFourSite 5: [ OK ] UpdateGroups.waterFourSite (0 ms) 5: [ RUN ] UpdateGroups.fourAtomsWithSettle 5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 5: [ RUN ] UpdateGroups.waterFlexAngle 5: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 5: [ RUN ] UpdateGroups.twoMoltypes 5: [ OK ] UpdateGroups.twoMoltypes (0 ms) 5: [----------] 9 tests from UpdateGroups (0 ms total) 5: 5: [----------] 1 test from UpdateGroupsCog 5: [ RUN ] UpdateGroupsCog.ComputesCogs 5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 5: [----------] 1 test from UpdateGroupsCog (1 ms total) 5: 5: [----------] 84 tests from WithParameters/ConstraintsTest 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (7 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms) 5: [----------] 84 tests from WithParameters/ConstraintsTest (9 ms total) 5: 5: [----------] 11 tests from WithParameters/EnergyOutputTest 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 5: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (9 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (2 ms) 5: [----------] 11 tests from WithParameters/EnergyOutputTest (31 ms total) 5: 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 5: 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 5: 5: [----------] 16 tests from WithParameters/LeapFrogTest 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (4 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (7 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 5: [----------] 16 tests from WithParameters/LeapFrogTest (27 ms total) 5: 5: [----------] 13 tests from WithParameters/SettleTest 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 5: [----------] 13 tests from WithParameters/SettleTest (7 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 187 tests from 13 test cases ran. (76 ms total) 5: [ PASSED ] 187 tests. 5/54 Test #5: MdlibUnitTest ....................... Passed 0.11 sec test 6 Start 6: AppliedForcesUnitTest 6: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 6: Test timeout computed to be: 30 6: [==========] Running 20 tests from 4 test cases. 6: [----------] Global test environment set-up. 6: [----------] 2 tests from DensityFittingTest 6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms) 6: [ RUN ] DensityFittingTest.SingleAtom 6: [ OK ] DensityFittingTest.SingleAtom (0 ms) 6: [----------] 2 tests from DensityFittingTest (1 ms total) 6: 6: [----------] 8 tests from DensityFittingOptionsTest 6: [ RUN ] DensityFittingOptionsTest.DefaultParameters 6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 6: [ RUN ] DensityFittingOptionsTest.KvtToInternal 6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 6: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 6: 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest 6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 6: 6: [----------] 3 tests from ElectricFieldTest 6: [ RUN ] ElectricFieldTest.Static 6: [ OK ] ElectricFieldTest.Static (0 ms) 6: [ RUN ] ElectricFieldTest.Oscillating 6: [ OK ] ElectricFieldTest.Oscillating (0 ms) 6: [ RUN ] ElectricFieldTest.Pulsed 6: [ OK ] ElectricFieldTest.Pulsed (0 ms) 6: [----------] 3 tests from ElectricFieldTest (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 20 tests from 4 test cases ran. (2 ms total) 6: [ PASSED ] 20 tests. 6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.02 sec test 7 Start 7: CommandLineUnitTests 7: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 59 tests from 7 test cases. 7: [----------] Global test environment set-up. 7: [----------] 3 tests from CommandLineHelpModuleTest 7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 7: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 7: 7: [----------] 7 tests from CommandLineHelpWriterTest 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 7: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 7: 7: [----------] 6 tests from CommandLineModuleManagerTest 7: [ RUN ] CommandLineModuleManagerTest.RunsModule 7: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 7: [----------] 6 tests from CommandLineModuleManagerTest (1 ms total) 7: 7: [----------] 13 tests from CommandLineParserTest 7: [ RUN ] CommandLineParserTest.HandlesSingleValues 7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesString 7: [ OK ] CommandLineParserTest.HandlesString (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 7: [----------] 13 tests from CommandLineParserTest (0 ms total) 7: 7: [----------] 6 tests from CommandLineProgramContextTest 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 7: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 7: 7: [----------] 3 tests from OutputNamesTest 7: [ RUN ] OutputNamesTest.CanBeSuffixed 7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 7: [----------] 3 tests from OutputNamesTest (0 ms total) 7: 7: [----------] 21 tests from ParseCommonArgsTest 7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (3 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 7: [----------] 21 tests from ParseCommonArgsTest (4 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 59 tests from 7 test cases ran. (8 ms total) 7: [ PASSED ] 59 tests. 7/54 Test #7: CommandLineUnitTests ................ Passed 0.03 sec test 8 Start 8: DomDecTests 8: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/DomDecTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 9 tests from 2 test cases. 8: [----------] Global test environment set-up. 8: [----------] 7 tests from HashedMap 8: [ RUN ] HashedMap.InsertsFinds 8: [ OK ] HashedMap.InsertsFinds (0 ms) 8: [ RUN ] HashedMap.NegativeKeysWork 8: [ OK ] HashedMap.NegativeKeysWork (0 ms) 8: [ RUN ] HashedMap.InsertsErases 8: [ OK ] HashedMap.InsertsErases (0 ms) 8: [ RUN ] HashedMap.InsertsOrAssigns 8: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 8: [ RUN ] HashedMap.Clears 8: [ OK ] HashedMap.Clears (0 ms) 8: [ RUN ] HashedMap.LinkedEntries 8: [ OK ] HashedMap.LinkedEntries (0 ms) 8: [ RUN ] HashedMap.ResizesTable 8: [ OK ] HashedMap.ResizesTable (0 ms) 8: [----------] 7 tests from HashedMap (1 ms total) 8: 8: [----------] 2 tests from LocalAtomSetManager 8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 8: [----------] 2 tests from LocalAtomSetManager (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 9 tests from 2 test cases ran. (1 ms total) 8: [ PASSED ] 9 tests. 8/54 Test #8: DomDecTests ......................... Passed 0.02 sec test 9 Start 9: EwaldUnitTests 9: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/EwaldUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 257 tests from 10 test cases. 9: [----------] Global test environment set-up. 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (3 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (3 ms total) 9: 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (6 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (4 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (5 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (87 ms total) 9: 9: [----------] 144 tests from SaneInput/PmeGatherTest 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (5 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (5 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (5 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (5 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (5 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (0 ms) 9: [----------] 144 tests from SaneInput/PmeGatherTest (88 ms total) 9: 9: [----------] 16 tests from SaneInput/PmeSolveTest 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (5 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (6 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (5 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (5 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (1 ms) 9: [----------] 16 tests from SaneInput/PmeSolveTest (33 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (5 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (5 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (14 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (6 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (5 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (17 ms total) 9: 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (5 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (5 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (5 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (1 ms) 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (32 ms total) 9: 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (7 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (5 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (1 ms) 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (37 ms total) 9: 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (6 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (6 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (36 ms total) 9: 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (7 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (7 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (8 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (9 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (14 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (15 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (7 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (8 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (9 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (13 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (5 ms) 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (108 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 257 tests from 10 test cases ran. (602 ms total) 9: [ PASSED ] 257 tests. 9/54 Test #9: EwaldUnitTests ...................... Passed 0.67 sec test 10 Start 10: FFTUnitTests 10: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/FFTUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 14 tests from 4 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from ManyFFTTest 10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (17 ms) 10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (66 ms) 10: [----------] 2 tests from ManyFFTTest (84 ms total) 10: 10: [----------] 1 test from FFTTest 10: [ RUN ] FFTTest.Real2DLength18_15Test 10: [ OK ] FFTTest.Real2DLength18_15Test (16 ms) 10: [----------] 1 test from FFTTest (16 ms total) 10: 10: [----------] 1 test from FFFTest3D 10: [ RUN ] FFFTest3D.Real5_6_9 10: [ OK ] FFFTest3D.Real5_6_9 (2 ms) 10: [----------] 1 test from FFFTest3D (3 ms total) 10: 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (8 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (2 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (5 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (10 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (32 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (47 ms) 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (108 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 14 tests from 4 test cases ran. (211 ms total) 10: [ PASSED ] 14 tests. 10/54 Test #10: FFTUnitTests ........................ Passed 0.25 sec test 11 Start 11: GpuUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 62 tests from 20 test cases. 11: [----------] Global test environment set-up. 11: [----------] 2 tests from ClfftInitializer 11: [ RUN ] ClfftInitializer.SingleInitializationWorks 11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 11: [ RUN ] ClfftInitializer.TwoInitializationsWork 11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 11: [----------] 2 tests from ClfftInitializer (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Swap 11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Comparison 11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Swap 11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Comparison 11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Swap 11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Comparison 11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Swap 11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Comparison 11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 11: 11: [----------] 1 test from HostAllocatorUntypedTest 11: [ RUN ] HostAllocatorUntypedTest.Comparison 11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (4 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/0 (4 ms total) 11: 11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/1 (1 ms total) 11: 11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/3 (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 62 tests from 20 test cases ran. (5 ms total) 11: [ PASSED ] 62 tests. 11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.04 sec test 12 Start 12: HardwareUnitTests 12: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/HardwareUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 4 tests from 1 test case. 12: [----------] Global test environment set-up. 12: [----------] 4 tests from HardwareTopologyTest 12: [ RUN ] HardwareTopologyTest.Execute 12: [ OK ] HardwareTopologyTest.Execute (104 ms) 12: [ RUN ] HardwareTopologyTest.HwlocExecute 12: [ OK ] HardwareTopologyTest.HwlocExecute (99 ms) 12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (101 ms) 12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (91 ms) 12: [----------] 4 tests from HardwareTopologyTest (396 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 4 tests from 1 test case ran. (396 ms total) 12: [ PASSED ] 4 tests. 12/54 Test #12: HardwareUnitTests ................... Passed 0.44 sec test 13 Start 13: MathUnitTests 13: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MathUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 204 tests from 29 test cases. 13: [----------] Global test environment set-up. 13: [----------] 1 test from EmptyArrayRefWithPaddingTest 13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 13: 13: [----------] 8 tests from TranslateAndScaleTest 13: [ RUN ] TranslateAndScaleTest.identityTransformation 13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingIdentity 13: [ OK ] TranslateAndScaleTest.scalingIdentity (1 ms) 13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 13: [----------] 8 tests from TranslateAndScaleTest (1 ms total) 13: 13: [----------] 12 tests from DensitySimilarityTest 13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (53 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (49 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (39 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 13: [----------] 12 tests from DensitySimilarityTest (141 ms total) 13: 13: [----------] 6 tests from StructureSimilarityTest 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 13: [----------] 6 tests from StructureSimilarityTest (0 ms total) 13: 13: [----------] 8 tests from ExponentialMovingAverage 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 13: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 13: 13: [----------] 21 tests from FunctionTest 13: [ RUN ] FunctionTest.StaticLog2 13: [ OK ] FunctionTest.StaticLog2 (0 ms) 13: [ RUN ] FunctionTest.Log2I32Bit 13: [ OK ] FunctionTest.Log2I32Bit (0 ms) 13: [ RUN ] FunctionTest.Log2I64Bit 13: [ OK ] FunctionTest.Log2I64Bit (0 ms) 13: [ RUN ] FunctionTest.GreatestCommonDivisor 13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 13: [ RUN ] FunctionTest.InvsqrtFloat 13: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvsqrtDouble 13: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvsqrtInteger 13: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 13: [ RUN ] FunctionTest.InvcbrtFloat 13: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvcbrtDouble 13: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvcbrtInteger 13: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 13: [ RUN ] FunctionTest.SixthrootFloat 13: [ OK ] FunctionTest.SixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.SixthrootDouble 13: [ OK ] FunctionTest.SixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.SixthrootInteger 13: [ OK ] FunctionTest.SixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootFloat 13: [ OK ] FunctionTest.InvsixthrootFloat (8 ms) 13: [ RUN ] FunctionTest.InvsixthrootDouble 13: [ OK ] FunctionTest.InvsixthrootDouble (1 ms) 13: [ RUN ] FunctionTest.InvsixthrootInteger 13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.Powers 13: [ OK ] FunctionTest.Powers (0 ms) 13: [ RUN ] FunctionTest.ErfInvFloat 13: [ OK ] FunctionTest.ErfInvFloat (0 ms) 13: [ RUN ] FunctionTest.ErfInvDouble 13: [ OK ] FunctionTest.ErfInvDouble (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 13: [----------] 21 tests from FunctionTest (10 ms total) 13: 13: [----------] 4 tests from GaussianOn1DLattice 13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 13: [ RUN ] GaussianOn1DLattice.isCorrect 13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 13: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 13: 13: [----------] 9 tests from GaussTransformTest 13: [ RUN ] GaussTransformTest.isZeroUponConstruction 13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (1 ms) 13: [ RUN ] GaussTransformTest.view 13: [ OK ] GaussTransformTest.view (0 ms) 13: [----------] 9 tests from GaussTransformTest (1 ms total) 13: 13: [----------] 3 tests from DensityFittingForce 13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 13: [ RUN ] DensityFittingForce.pullsTowardsDerivative 13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 13: [----------] 3 tests from DensityFittingForce (0 ms total) 13: 13: [----------] 2 tests from InvertMatrixTest 13: [ RUN ] InvertMatrixTest.IdentityIsImpotent 13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertMatrixTest.ComputesInverse 13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 13: [----------] 2 tests from InvertMatrixTest (0 ms total) 13: 13: [----------] 2 tests from InvertBoxMatrixTest 13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 13: 13: [----------] 15 tests from MatrixTest 13: [ RUN ] MatrixTest.canSetFromArray 13: [ OK ] MatrixTest.canSetFromArray (0 ms) 13: [ RUN ] MatrixTest.canSetStaticallyFromList 13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 13: [ RUN ] MatrixTest.canConstructAndFill 13: [ OK ] MatrixTest.canConstructAndFill (0 ms) 13: [ RUN ] MatrixTest.canSetValues 13: [ OK ] MatrixTest.canSetValues (0 ms) 13: [ RUN ] MatrixTest.canCopyAssign 13: [ OK ] MatrixTest.canCopyAssign (0 ms) 13: [ RUN ] MatrixTest.canSwap 13: [ OK ] MatrixTest.canSwap (0 ms) 13: [ RUN ] MatrixTest.staticMultiDimArrayExtent 13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MatrixTest.determinantWorks 13: [ OK ] MatrixTest.determinantWorks (0 ms) 13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 13: [ RUN ] MatrixTest.traceWorks 13: [ OK ] MatrixTest.traceWorks (0 ms) 13: [ RUN ] MatrixTest.transposeWorks 13: [ OK ] MatrixTest.transposeWorks (0 ms) 13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 13: [ RUN ] MatrixTest.canFillLegacyMatrix 13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 13: [----------] 15 tests from MatrixTest (0 ms total) 13: 13: [----------] 25 tests from MultiDimArrayTest 13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapStatic 13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapDynamic 13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToView 13: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToConstView 13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 13: [ RUN ] MultiDimArrayTest.viewBegin 13: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.viewEnd 13: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstBegin 13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstEnd 13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 13: [----------] 25 tests from MultiDimArrayTest (0 ms total) 13: 13: [----------] 4 tests from MultiDimArrayToMdSpanTest 13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanCopyAssign 13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanMoveAssign 13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanSwap 13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanCopyAssign 13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanMoveAssign 13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanSwap 13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanCopyAssign 13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanMoveAssign 13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanSwap 13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanCopyAssign 13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanMoveAssign 13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanSwap 13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanCopyAssign 13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanMoveAssign 13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanSwap 13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanCopyAssign 13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanMoveAssign 13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanSwap 13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanCopyAssign 13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanMoveAssign 13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanSwap 13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/6 (1 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanCopyAssign 13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanMoveAssign 13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanSwap 13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanCopyAssign 13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanMoveAssign 13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanSwap 13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanCopyAssign 13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanMoveAssign 13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanSwap 13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 13: 13: [----------] 37 tests from RVecTest 13: [ RUN ] RVecTest.CanBeStoredInVector 13: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAsMutable_rvec 13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Array 13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 13: [ RUN ] RVecTest.CanAddRVecToRvec 13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanAddAssignRVecToRvec 13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractRVecFromRvec 13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanDotProductRVecByRvec 13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanCrossProductRVecByRvec 13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVecInplace 13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 13: [ RUN ] RVecTest.CanScaleRVec 13: [ OK ] RVecTest.CanScaleRVec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVec 13: [ OK ] RVecTest.CanDivideRVec (0 ms) 13: [ RUN ] RVecTest.CanDoUnitvFromRVec 13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanSqLengthOfRVec 13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanLengthOfRVec 13: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToRVec 13: [ OK ] RVecTest.CanCastToRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToDVec 13: [ OK ] RVecTest.CanCastToDVec (0 ms) 13: [ RUN ] RVecTest.CanLeftScalarMultiply 13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanRightScalarMultiply 13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanGetUnitvFromRVec 13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanGetSqLengthOfRVec 13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanGetLengthOfRVec 13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoCrossProductOfRVec 13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoDotProductOfRVec 13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanScaleByVector 13: [ OK ] RVecTest.CanScaleByVector (0 ms) 13: [ RUN ] RVecTest.asIVec 13: [ OK ] RVecTest.asIVec (0 ms) 13: [ RUN ] RVecTest.elementWiseMin 13: [ OK ] RVecTest.elementWiseMin (0 ms) 13: [ RUN ] RVecTest.elementWiseMax 13: [ OK ] RVecTest.elementWiseMax (0 ms) 13: [ RUN ] RVecTest.WorksAs_dvec_Reference 13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_ivec_Reference 13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Reference 13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 13: [ RUN ] RVecTest.CopyConstructorWorks 13: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 13: [ RUN ] RVecTest.CopyAssignmentWorks 13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] RVecTest.MoveConstructorWorks 13: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 13: [ RUN ] RVecTest.MoveAssignmentWorks 13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 13: [----------] 37 tests from RVecTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 204 tests from 29 test cases ran. (154 ms total) 13: [ PASSED ] 204 tests. 13/54 Test #13: MathUnitTests ....................... Passed 0.20 sec test 14 Start 14: MdrunUtilityUnitTests 14: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 17 tests from 1 test case. 14: [----------] Global test environment set-up. 14: [----------] 17 tests from ThreadAffinityTest 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 14: NOTE: Affinity setting failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (18 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (4 ms) 14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (12 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 14: NOTE: Affinity setting for 1/2 threads failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (16 ms) 14: [----------] 17 tests from ThreadAffinityTest (52 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 17 tests from 1 test case ran. (52 ms total) 14: [ PASSED ] 17 tests. 14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.10 sec test 15 Start 15: MdrunUtilityMpiUnitTests 15: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 13 tests from 2 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from ThreadAffinityMultiRankTest 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (67 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (72 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (64 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (57 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (174 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (117 ms) 15: [----------] 6 tests from ThreadAffinityMultiRankTest (552 ms total) 15: 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (86 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (120 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (86 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (134 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (38 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (49 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (113 ms) 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (627 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 13 tests from 2 test cases ran. (1179 ms total) 15: [ PASSED ] 13 tests. 15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 1.22 sec test 16 Start 16: MDSpanTests 16: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MDSpanTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 32 tests from 7 test cases. 16: [----------] Global test environment set-up. 16: [----------] 4 tests from BasicAccessorPolicy 16: [ RUN ] BasicAccessorPolicy.Decay 16: [ OK ] BasicAccessorPolicy.Decay (0 ms) 16: [ RUN ] BasicAccessorPolicy.Access 16: [ OK ] BasicAccessorPolicy.Access (0 ms) 16: [ RUN ] BasicAccessorPolicy.Offset 16: [ OK ] BasicAccessorPolicy.Offset (0 ms) 16: [ RUN ] BasicAccessorPolicy.CopyAccessor 16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 16: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 16: 16: [----------] 4 tests from ExtentsTest 16: [ RUN ] ExtentsTest.Construction 16: [ OK ] ExtentsTest.Construction (0 ms) 16: [ RUN ] ExtentsTest.PurelyStatic 16: [ OK ] ExtentsTest.PurelyStatic (0 ms) 16: [ RUN ] ExtentsTest.RankNought 16: [ OK ] ExtentsTest.RankNought (0 ms) 16: [ RUN ] ExtentsTest.Assignment 16: [ OK ] ExtentsTest.Assignment (0 ms) 16: [----------] 4 tests from ExtentsTest (0 ms total) 16: 16: [----------] 8 tests from MdSpanExtension 16: [ RUN ] MdSpanExtension.SlicingAllStatic 16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingDynamic 16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingAllStatic3D 16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 16: [ RUN ] MdSpanExtension.SlicingEqualsView3D 16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 16: [ RUN ] MdSpanExtension.additionWorks 16: [ OK ] MdSpanExtension.additionWorks (0 ms) 16: [ RUN ] MdSpanExtension.subtractionWorks 16: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 16: [ RUN ] MdSpanExtension.multiplicationWorks 16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 16: [ RUN ] MdSpanExtension.divisionWorks 16: [ OK ] MdSpanExtension.divisionWorks (0 ms) 16: [----------] 8 tests from MdSpanExtension (0 ms total) 16: 16: [----------] 3 tests from LayoutTests 16: [ RUN ] LayoutTests.LayoutRightConstruction 16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 16: [ RUN ] LayoutTests.LayoutRightProperties 16: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 16: [ RUN ] LayoutTests.LayoutRightOperator 16: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 16: [----------] 3 tests from LayoutTests (0 ms total) 16: 16: [----------] 1 test from MdSpanTest 16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 16: [----------] 1 test from MdSpanTest (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/0.Rank 16: [ OK ] MdSpanTest/0.Rank (0 ms) 16: [ RUN ] MdSpanTest/0.DynamicRank 16: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/0.Extents 16: [ OK ] MdSpanTest/0.Extents (0 ms) 16: [ RUN ] MdSpanTest/0.Strides 16: [ OK ] MdSpanTest/0.Strides (0 ms) 16: [ RUN ] MdSpanTest/0.Properties 16: [ OK ] MdSpanTest/0.Properties (0 ms) 16: [ RUN ] MdSpanTest/0.Operator 16: [ OK ] MdSpanTest/0.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/0 (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/1.Rank 16: [ OK ] MdSpanTest/1.Rank (0 ms) 16: [ RUN ] MdSpanTest/1.DynamicRank 16: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/1.Extents 16: [ OK ] MdSpanTest/1.Extents (0 ms) 16: [ RUN ] MdSpanTest/1.Strides 16: [ OK ] MdSpanTest/1.Strides (0 ms) 16: [ RUN ] MdSpanTest/1.Properties 16: [ OK ] MdSpanTest/1.Properties (0 ms) 16: [ RUN ] MdSpanTest/1.Operator 16: [ OK ] MdSpanTest/1.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/1 (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 32 tests from 7 test cases ran. (0 ms total) 16: [ PASSED ] 32 tests. 16/54 Test #16: MDSpanTests ......................... Passed 0.02 sec test 17 Start 17: OnlineHelpUnitTests 17: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 22 tests from 4 test cases. 17: [----------] Global test environment set-up. 17: [----------] 6 tests from TextTableFormatterTest 17: [ RUN ] TextTableFormatterTest.HandlesBasicCase 17: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesIndentation 17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 17: [----------] 6 tests from TextTableFormatterTest (0 ms total) 17: 17: [----------] 3 tests from HelpManagerTest 17: [ RUN ] HelpManagerTest.HandlesRootTopic 17: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 17: [ RUN ] HelpManagerTest.HandlesSubTopics 17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 17: [ RUN ] HelpManagerTest.HandlesInvalidTopics 17: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms) 17: [----------] 3 tests from HelpManagerTest (1 ms total) 17: 17: [----------] 2 tests from HelpTopicFormattingTest 17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 17: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 17: 17: [----------] 11 tests from HelpWriterContextTest 17: [ RUN ] HelpWriterContextTest.FormatsParagraphs 17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralText 17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsBulletList 17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms) 17: [ RUN ] HelpWriterContextTest.FormatsGridTable 17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsTitles 17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 17: [----------] 11 tests from HelpWriterContextTest (1 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 22 tests from 4 test cases ran. (2 ms total) 17: [ PASSED ] 22 tests. 17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.03 sec test 18 Start 18: OptionsUnitTests 18: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/OptionsUnitTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 110 tests from 18 test cases. 18: [----------] Global test environment set-up. 18: [----------] 5 tests from AbstractOptionStorageTest 18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 18: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 18: 18: [----------] 8 tests from FileNameOptionTest 18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 18: [----------] 8 tests from FileNameOptionTest (0 ms total) 18: 18: [----------] 15 tests from FileNameOptionManagerTest 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 18: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 18: 18: [----------] 1 test from OptionsTest 18: [ RUN ] OptionsTest.FailsOnNonsafeStorage 18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 18: [----------] 1 test from OptionsTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerTest 18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMissingValue 18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesExtraValue 18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesGroups 18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesSections 18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 18: [----------] 9 tests from OptionsAssignerTest (1 ms total) 18: 18: [----------] 4 tests from OptionsAssignerBooleanTest 18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 18: 18: [----------] 13 tests from OptionsAssignerIntegerTest 18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 18: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 18: 18: [----------] 5 tests from OptionsAssignerDoubleTest 18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerStringTest 18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 18: 18: [----------] 6 tests from OptionsAssignerEnumTest 18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (3 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 6 tests from OptionsAssignerEnumTest (3 ms total) 18: 18: [----------] 8 tests from RepeatingOptionSectionTest 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (1 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 18: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total) 18: 18: [----------] 1 test from TimeUnitManagerTest 18: [ RUN ] TimeUnitManagerTest.BasicOperations 18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 18: [----------] 1 test from TimeUnitManagerTest (0 ms total) 18: 18: [----------] 4 tests from TimeUnitBehaviorTest 18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 18: 18: [----------] 2 tests from TreeValueSupportAssignTest 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 18: 18: [----------] 1 test from TreeValueSupportAssignErrorTest 18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 18: 18: [----------] 5 tests from TreeValueSupportCheckTest 18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 18: 18: [----------] 6 tests from TreeValueSupportAdjustTest 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms) 18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 18: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 18: 18: [----------] 8 tests from TreeValueSupportTest 18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsInt64Option 18: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsStringOption 18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsFloatOption 18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumOption 18: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 18: [----------] 8 tests from TreeValueSupportTest (1 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 110 tests from 18 test cases ran. (8 ms total) 18: [ PASSED ] 110 tests. 18/54 Test #18: OptionsUnitTests .................... Passed 0.07 sec test 19 Start 19: PbcutilUnitTest 19: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 19: Test timeout computed to be: 30 19: [==========] Running 3 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 1 test from PbcTest 19: [ RUN ] PbcTest.CalcShiftsWorks 19: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 19: [----------] 1 test from PbcTest (0 ms total) 19: 19: [----------] 2 tests from PbcEnumsTest 19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 19: [----------] 2 tests from PbcEnumsTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 3 tests from 2 test cases ran. (0 ms total) 19: [ PASSED ] 3 tests. 19/54 Test #19: PbcutilUnitTest ..................... Passed 0.02 sec test 20 Start 20: RandomUnitTests 20: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/RandomUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 44 tests from 10 test cases. 20: [----------] Global test environment set-up. 20: [----------] 4 tests from ExponentialDistributionTest 20: [ RUN ] ExponentialDistributionTest.Output 20: [ OK ] ExponentialDistributionTest.Output (0 ms) 20: [ RUN ] ExponentialDistributionTest.Logical 20: [ OK ] ExponentialDistributionTest.Logical (0 ms) 20: [ RUN ] ExponentialDistributionTest.Reset 20: [ OK ] ExponentialDistributionTest.Reset (0 ms) 20: [ RUN ] ExponentialDistributionTest.AltParam 20: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 20: 20: [----------] 4 tests from GammaDistributionTest 20: [ RUN ] GammaDistributionTest.Output 20: [ OK ] GammaDistributionTest.Output (0 ms) 20: [ RUN ] GammaDistributionTest.Logical 20: [ OK ] GammaDistributionTest.Logical (0 ms) 20: [ RUN ] GammaDistributionTest.Reset 20: [ OK ] GammaDistributionTest.Reset (0 ms) 20: [ RUN ] GammaDistributionTest.AltParam 20: [ OK ] GammaDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from GammaDistributionTest (0 ms total) 20: 20: [----------] 4 tests from NormalDistributionTest 20: [ RUN ] NormalDistributionTest.Output 20: [ OK ] NormalDistributionTest.Output (0 ms) 20: [ RUN ] NormalDistributionTest.Logical 20: [ OK ] NormalDistributionTest.Logical (0 ms) 20: [ RUN ] NormalDistributionTest.Reset 20: [ OK ] NormalDistributionTest.Reset (0 ms) 20: [ RUN ] NormalDistributionTest.AltParam 20: [ OK ] NormalDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from NormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from SeedTest 20: [ RUN ] SeedTest.makeRandomSeed 20: [ OK ] SeedTest.makeRandomSeed (0 ms) 20: [----------] 1 test from SeedTest (0 ms total) 20: 20: [----------] 6 tests from TabulatedNormalDistributionTest 20: [ RUN ] TabulatedNormalDistributionTest.Output14 20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Output16 20: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Logical 20: [ OK ] TabulatedNormalDistributionTest.Logical (1 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Reset 20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.AltParam 20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 20: [----------] 6 tests from TabulatedNormalDistributionTest (4 ms total) 20: 20: [----------] 1 test from TabulatedNormalDistributionTableTest 20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (1 ms) 20: [----------] 1 test from TabulatedNormalDistributionTableTest (1 ms total) 20: 20: [----------] 6 tests from ThreeFry2x64Test 20: [ RUN ] ThreeFry2x64Test.Logical 20: [ OK ] ThreeFry2x64Test.Logical (0 ms) 20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 20: [ RUN ] ThreeFry2x64Test.Reseed 20: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 20: [ RUN ] ThreeFry2x64Test.Discard 20: [ OK ] ThreeFry2x64Test.Discard (0 ms) 20: [ RUN ] ThreeFry2x64Test.InvalidCounter 20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 20: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 20: 20: [----------] 4 tests from UniformIntDistributionTest 20: [ RUN ] UniformIntDistributionTest.Output 20: [ OK ] UniformIntDistributionTest.Output (0 ms) 20: [ RUN ] UniformIntDistributionTest.Logical 20: [ OK ] UniformIntDistributionTest.Logical (0 ms) 20: [ RUN ] UniformIntDistributionTest.Reset 20: [ OK ] UniformIntDistributionTest.Reset (0 ms) 20: [ RUN ] UniformIntDistributionTest.AltParam 20: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 20: 20: [----------] 5 tests from UniformRealDistributionTest 20: [ RUN ] UniformRealDistributionTest.GenerateCanonical 20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Output 20: [ OK ] UniformRealDistributionTest.Output (0 ms) 20: [ RUN ] UniformRealDistributionTest.Logical 20: [ OK ] UniformRealDistributionTest.Logical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Reset 20: [ OK ] UniformRealDistributionTest.Reset (0 ms) 20: [ RUN ] UniformRealDistributionTest.AltParam 20: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 20: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 20: 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 44 tests from 10 test cases ran. (8 ms total) 20: [ PASSED ] 44 tests. 20/54 Test #20: RandomUnitTests ..................... Passed 0.04 sec test 21 Start 21: RestraintTests 21: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/RestraintTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 1 test from 1 test case. 21: [----------] Global test environment set-up. 21: [----------] 1 test from RestraintManager 21: [ RUN ] RestraintManager.restraintList 21: [ OK ] RestraintManager.restraintList (0 ms) 21: [----------] 1 test from RestraintManager (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1 test from 1 test case ran. (0 ms total) 21: [ PASSED ] 1 test. 21/54 Test #21: RestraintTests ...................... Passed 0.02 sec test 22 Start 22: TableUnitTests 22: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/TableUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 20 tests from 2 test cases. 22: [----------] Global test environment set-up. 22: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms) 22: [ RUN ] SplineTableTest/0.Sinc 22: [ OK ] SplineTableTest/0.Sinc (0 ms) 22: [ RUN ] SplineTableTest/0.LJ12 22: [ OK ] SplineTableTest/0.LJ12 (17 ms) 22: [ RUN ] SplineTableTest/0.PmeCorrection 22: [ OK ] SplineTableTest/0.PmeCorrection (2 ms) 22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/0.TwoFunctions 22: [ OK ] SplineTableTest/0.TwoFunctions (31 ms) 22: [ RUN ] SplineTableTest/0.ThreeFunctions 22: [ OK ] SplineTableTest/0.ThreeFunctions (32 ms) 22: [ RUN ] SplineTableTest/0.Simd 22: [ OK ] SplineTableTest/0.Simd (7 ms) 22: [ RUN ] SplineTableTest/0.SimdTwoFunctions 22: [ OK ] SplineTableTest/0.SimdTwoFunctions (26 ms) 22: [----------] 10 tests from SplineTableTest/0 (120 ms total) 22: 22: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 22: [ RUN ] SplineTableTest/1.Sinc 22: [ OK ] SplineTableTest/1.Sinc (0 ms) 22: [ RUN ] SplineTableTest/1.LJ12 22: [ OK ] SplineTableTest/1.LJ12 (2 ms) 22: [ RUN ] SplineTableTest/1.PmeCorrection 22: [ OK ] SplineTableTest/1.PmeCorrection (2 ms) 22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/1.TwoFunctions 22: [ OK ] SplineTableTest/1.TwoFunctions (3 ms) 22: [ RUN ] SplineTableTest/1.ThreeFunctions 22: [ OK ] SplineTableTest/1.ThreeFunctions (5 ms) 22: [ RUN ] SplineTableTest/1.Simd 22: [ OK ] SplineTableTest/1.Simd (1 ms) 22: [ RUN ] SplineTableTest/1.SimdTwoFunctions 22: [ OK ] SplineTableTest/1.SimdTwoFunctions (4 ms) 22: [----------] 10 tests from SplineTableTest/1 (19 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 20 tests from 2 test cases ran. (139 ms total) 22: [ PASSED ] 20 tests. 22/54 Test #22: TableUnitTests ...................... Passed 0.16 sec test 23 Start 23: TaskAssignmentUnitTests 23: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 2 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms) 23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (1 ms total) 23: 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 2 test cases ran. (1 ms total) 23: [ PASSED ] 3 tests. 23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.02 sec test 24 Start 24: TopologyTest 24: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/TopologyTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 11 tests from 3 test cases. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ExclusionBlockTest 24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 24: [ RUN ] ExclusionBlockTest.MergeExclusions 24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 24: [----------] 3 tests from ExclusionBlockTest (0 ms total) 24: 24: [----------] 2 tests from MtopTest 24: [ RUN ] MtopTest.RangeBasedLoop 24: [ OK ] MtopTest.RangeBasedLoop (0 ms) 24: [ RUN ] MtopTest.Operators 24: [ OK ] MtopTest.Operators (0 ms) 24: [----------] 2 tests from MtopTest (0 ms total) 24: 24: [----------] 6 tests from SymtabTest 24: [ RUN ] SymtabTest.EmptyOnOpen 24: [ OK ] SymtabTest.EmptyOnOpen (0 ms) 24: [ RUN ] SymtabTest.AddSingleEntry 24: [ OK ] SymtabTest.AddSingleEntry (0 ms) 24: [ RUN ] SymtabTest.AddTwoDistinctEntries 24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms) 24: [ RUN ] SymtabTest.TryToAddDuplicates 24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms) 24: [ RUN ] SymtabTest.AddLargeNumberOfEntries 24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms) 24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable 24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms) 24: [----------] 6 tests from SymtabTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 11 tests from 3 test cases ran. (0 ms total) 24: [ PASSED ] 11 tests. 24/54 Test #24: TopologyTest ........................ Passed 0.03 sec test 25 Start 25: PullTest 25: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/PullTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 5 tests from 1 test case. 25: [----------] Global test environment set-up. 25: [----------] 5 tests from PullTest 25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 25: [----------] 5 tests from PullTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 5 tests from 1 test case ran. (4 ms total) 25: [ PASSED ] 5 tests. 25/54 Test #25: PullTest ............................ Passed 0.04 sec test 26 Start 26: AwhTest 26: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/AwhTest.xml" 26: Test timeout computed to be: 30 26: [==========] Running 12 tests from 4 test cases. 26: [----------] Global test environment set-up. 26: [----------] 1 test from BiasTest 26: [ RUN ] BiasTest.DetectsCovering 26: [ OK ] BiasTest.DetectsCovering (0 ms) 26: [----------] 1 test from BiasTest (0 ms total) 26: 26: [----------] 1 test from gridTest 26: [ RUN ] gridTest.neighborhood 26: [ OK ] gridTest.neighborhood (2 ms) 26: [----------] 1 test from gridTest (2 ms total) 26: 26: [----------] 8 tests from WithParameters/BiasTest 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) 26: [----------] 8 tests from WithParameters/BiasTest (3 ms total) 26: 26: [----------] 2 tests from WithParameters/BiasStateTest 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms) 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 26: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 12 tests from 4 test cases ran. (6 ms total) 26: [ PASSED ] 12 tests. 26/54 Test #26: AwhTest ............................. Passed 0.03 sec test 27 Start 27: SimdUnitTests 27: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/SimdUnitTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 288 tests from 22 test cases. 27: [----------] Global test environment set-up. 27: [----------] 9 tests from SimdBootstrapTest 27: [ RUN ] SimdBootstrapTest.loadStore 27: [ OK ] SimdBootstrapTest.loadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.loadU 27: [ OK ] SimdBootstrapTest.loadU (0 ms) 27: [ RUN ] SimdBootstrapTest.storeU 27: [ OK ] SimdBootstrapTest.storeU (0 ms) 27: [ RUN ] SimdBootstrapTest.loadStoreI 27: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 27: [ RUN ] SimdBootstrapTest.loadUI 27: [ OK ] SimdBootstrapTest.loadUI (0 ms) 27: [ RUN ] SimdBootstrapTest.storeUI 27: [ OK ] SimdBootstrapTest.storeUI (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadStore 27: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadU 27: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4StoreU 27: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 27: [----------] 9 tests from SimdBootstrapTest (0 ms total) 27: 27: [----------] 1 test from SimdTest 27: [ RUN ] SimdTest.GmxAligned 27: [ OK ] SimdTest.GmxAligned (0 ms) 27: [----------] 1 test from SimdTest (0 ms total) 27: 27: [----------] 42 tests from SimdFloatingpointTest 27: [ RUN ] SimdFloatingpointTest.setZero 27: [ OK ] SimdFloatingpointTest.setZero (0 ms) 27: [ RUN ] SimdFloatingpointTest.set 27: [ OK ] SimdFloatingpointTest.set (0 ms) 27: [ RUN ] SimdFloatingpointTest.add 27: [ OK ] SimdFloatingpointTest.add (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskAdd 27: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 27: [ RUN ] SimdFloatingpointTest.sub 27: [ OK ] SimdFloatingpointTest.sub (0 ms) 27: [ RUN ] SimdFloatingpointTest.mul 27: [ OK ] SimdFloatingpointTest.mul (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzMul 27: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 27: [ RUN ] SimdFloatingpointTest.fma 27: [ OK ] SimdFloatingpointTest.fma (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzFma 27: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fms 27: [ OK ] SimdFloatingpointTest.fms (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnma 27: [ OK ] SimdFloatingpointTest.fnma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnms 27: [ OK ] SimdFloatingpointTest.fnms (0 ms) 27: [ RUN ] SimdFloatingpointTest.abs 27: [ OK ] SimdFloatingpointTest.abs (0 ms) 27: [ RUN ] SimdFloatingpointTest.neg 27: [ OK ] SimdFloatingpointTest.neg (0 ms) 27: [ RUN ] SimdFloatingpointTest.and 27: [ OK ] SimdFloatingpointTest.and (0 ms) 27: [ RUN ] SimdFloatingpointTest.or 27: [ OK ] SimdFloatingpointTest.or (0 ms) 27: [ RUN ] SimdFloatingpointTest.xor 27: [ OK ] SimdFloatingpointTest.xor (0 ms) 27: [ RUN ] SimdFloatingpointTest.andNot 27: [ OK ] SimdFloatingpointTest.andNot (0 ms) 27: [ RUN ] SimdFloatingpointTest.max 27: [ OK ] SimdFloatingpointTest.max (0 ms) 27: [ RUN ] SimdFloatingpointTest.min 27: [ OK ] SimdFloatingpointTest.min (0 ms) 27: [ RUN ] SimdFloatingpointTest.round 27: [ OK ] SimdFloatingpointTest.round (0 ms) 27: [ RUN ] SimdFloatingpointTest.roundMode 27: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 27: [ RUN ] SimdFloatingpointTest.trunc 27: [ OK ] SimdFloatingpointTest.trunc (0 ms) 27: [ RUN ] SimdFloatingpointTest.frexp 27: [ OK ] SimdFloatingpointTest.frexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.ldexp 27: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.rsqrt 27: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRsqrt 27: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.rcp 27: [ OK ] SimdFloatingpointTest.rcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRcp 27: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.selectByNotMask 27: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpNe 27: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLe 27: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLt 27: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 27: [ RUN ] SimdFloatingpointTest.testBits 27: [ OK ] SimdFloatingpointTest.testBits (0 ms) 27: [ RUN ] SimdFloatingpointTest.andB 27: [ OK ] SimdFloatingpointTest.andB (0 ms) 27: [ RUN ] SimdFloatingpointTest.orB 27: [ OK ] SimdFloatingpointTest.orB (0 ms) 27: [ RUN ] SimdFloatingpointTest.anyTrueB 27: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 27: [ RUN ] SimdFloatingpointTest.blend 27: [ OK ] SimdFloatingpointTest.blend (0 ms) 27: [ RUN ] SimdFloatingpointTest.reduce 27: [ OK ] SimdFloatingpointTest.reduce (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 27: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 27: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 27: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 27: 27: [----------] 16 tests from SimdFloatingpointUtilTest 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 27: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 27: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 27: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 27: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 27: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 27: [----------] 16 tests from SimdFloatingpointUtilTest (1 ms total) 27: 27: [----------] 3 tests from SimdVectorOperationsTest 27: [ RUN ] SimdVectorOperationsTest.iprod 27: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 27: [ RUN ] SimdVectorOperationsTest.norm2 27: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 27: [ RUN ] SimdVectorOperationsTest.cprod 27: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 27: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 27: 27: [----------] 56 tests from SimdMathTest 27: [ RUN ] SimdMathTest.generateTestPointsFloat 27: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 27: [ RUN ] SimdMathTest.copysign 27: [ OK ] SimdMathTest.copysign (0 ms) 27: [ RUN ] SimdMathTest.invsqrt 27: [ OK ] SimdMathTest.invsqrt (8 ms) 27: [ RUN ] SimdMathTest.maskzInvsqrt 27: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPair 27: [ OK ] SimdMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdMathTest.sqrt 27: [ OK ] SimdMathTest.sqrt (1 ms) 27: [ RUN ] SimdMathTest.sqrtUnsafe 27: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 27: [ RUN ] SimdMathTest.inv 27: [ OK ] SimdMathTest.inv (2 ms) 27: [ RUN ] SimdMathTest.maskzInv 27: [ OK ] SimdMathTest.maskzInv (0 ms) 27: [ RUN ] SimdMathTest.cbrt 27: [ OK ] SimdMathTest.cbrt (1 ms) 27: [ RUN ] SimdMathTest.invcbrt 27: [ OK ] SimdMathTest.invcbrt (2 ms) 27: [ RUN ] SimdMathTest.log2 27: [ OK ] SimdMathTest.log2 (0 ms) 27: [ RUN ] SimdMathTest.log 27: [ OK ] SimdMathTest.log (1 ms) 27: [ RUN ] SimdMathTest.exp2 27: [ OK ] SimdMathTest.exp2 (10 ms) 27: [ RUN ] SimdMathTest.exp2Unsafe 27: [ OK ] SimdMathTest.exp2Unsafe (1 ms) 27: [ RUN ] SimdMathTest.exp 27: [ OK ] SimdMathTest.exp (2 ms) 27: [ RUN ] SimdMathTest.expUnsafe 27: [ OK ] SimdMathTest.expUnsafe (1 ms) 27: [ RUN ] SimdMathTest.pow 27: [ OK ] SimdMathTest.pow (0 ms) 27: [ RUN ] SimdMathTest.powUnsafe 27: [ OK ] SimdMathTest.powUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erf 27: [ OK ] SimdMathTest.erf (1 ms) 27: [ RUN ] SimdMathTest.erfc 27: [ OK ] SimdMathTest.erfc (10 ms) 27: [ RUN ] SimdMathTest.sin 27: [ OK ] SimdMathTest.sin (1 ms) 27: [ RUN ] SimdMathTest.cos 27: [ OK ] SimdMathTest.cos (2 ms) 27: [ RUN ] SimdMathTest.tan 27: [ OK ] SimdMathTest.tan (1 ms) 27: [ RUN ] SimdMathTest.asin 27: [ OK ] SimdMathTest.asin (1 ms) 27: [ RUN ] SimdMathTest.acos 27: [ OK ] SimdMathTest.acos (1 ms) 27: [ RUN ] SimdMathTest.atan 27: [ OK ] SimdMathTest.atan (1 ms) 27: [ RUN ] SimdMathTest.atan2 27: [ OK ] SimdMathTest.atan2 (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrection 27: [ OK ] SimdMathTest.pmeForceCorrection (9 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrection 27: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracy 27: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (1 ms) 27: [ RUN ] SimdMathTest.invSingleAccuracy 27: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.cbrtSingleAccuracy 27: [ OK ] SimdMathTest.cbrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 27: [ OK ] SimdMathTest.invcbrtSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.log2SingleAccuracy 27: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.logSingleAccuracy 27: [ OK ] SimdMathTest.logSingleAccuracy (8 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracy 27: [ OK ] SimdMathTest.exp2SingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 27: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracy 27: [ OK ] SimdMathTest.expSingleAccuracy (3 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracy 27: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erfSingleAccuracy 27: [ OK ] SimdMathTest.erfSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.erfcSingleAccuracy 27: [ OK ] SimdMathTest.erfcSingleAccuracy (9 ms) 27: [ RUN ] SimdMathTest.sinSingleAccuracy 27: [ OK ] SimdMathTest.sinSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.cosSingleAccuracy 27: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.tanSingleAccuracy 27: [ OK ] SimdMathTest.tanSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.asinSingleAccuracy 27: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.acosSingleAccuracy 27: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atanSingleAccuracy 27: [ OK ] SimdMathTest.atanSingleAccuracy (8 ms) 27: [ RUN ] SimdMathTest.atan2SingleAccuracy 27: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (1 ms) 27: [----------] 56 tests from SimdMathTest (106 ms total) 27: 27: [----------] 1 test from EmptyArrayRefTest 27: [ RUN ] EmptyArrayRefTest.IsEmpty 27: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 27: [----------] 1 test from EmptyArrayRefTest (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/0.Assignment 27: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/1.Assignment 27: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/0.Basic 27: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/1.Basic 27: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 27: 27: [----------] 23 tests from SimdIntegerTest 27: [ RUN ] SimdIntegerTest.setZero 27: [ OK ] SimdIntegerTest.setZero (0 ms) 27: [ RUN ] SimdIntegerTest.set 27: [ OK ] SimdIntegerTest.set (0 ms) 27: [ RUN ] SimdIntegerTest.add 27: [ OK ] SimdIntegerTest.add (0 ms) 27: [ RUN ] SimdIntegerTest.sub 27: [ OK ] SimdIntegerTest.sub (0 ms) 27: [ RUN ] SimdIntegerTest.mul 27: [ OK ] SimdIntegerTest.mul (0 ms) 27: [ RUN ] SimdIntegerTest.and 27: [ OK ] SimdIntegerTest.and (0 ms) 27: [ RUN ] SimdIntegerTest.andNot 27: [ OK ] SimdIntegerTest.andNot (0 ms) 27: [ RUN ] SimdIntegerTest.or 27: [ OK ] SimdIntegerTest.or (0 ms) 27: [ RUN ] SimdIntegerTest.xor 27: [ OK ] SimdIntegerTest.xor (0 ms) 27: [ RUN ] SimdIntegerTest.extract 27: [ OK ] SimdIntegerTest.extract (0 ms) 27: [ RUN ] SimdIntegerTest.cvtR2I 27: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvttR2I 27: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvtI2R 27: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpLt 27: [ OK ] SimdIntegerTest.cmpLt (0 ms) 27: [ RUN ] SimdIntegerTest.testBits 27: [ OK ] SimdIntegerTest.testBits (0 ms) 27: [ RUN ] SimdIntegerTest.andB 27: [ OK ] SimdIntegerTest.andB (0 ms) 27: [ RUN ] SimdIntegerTest.orB 27: [ OK ] SimdIntegerTest.orB (0 ms) 27: [ RUN ] SimdIntegerTest.anyTrue 27: [ OK ] SimdIntegerTest.anyTrue (0 ms) 27: [ RUN ] SimdIntegerTest.blend 27: [ OK ] SimdIntegerTest.blend (0 ms) 27: [ RUN ] SimdIntegerTest.cvtB2IB 27: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 27: [ RUN ] SimdIntegerTest.cvtIB2B 27: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 27: [----------] 23 tests from SimdIntegerTest (0 ms total) 27: 27: [----------] 32 tests from Simd4FloatingpointTest 27: [ RUN ] Simd4FloatingpointTest.setZero 27: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 27: [ RUN ] Simd4FloatingpointTest.set 27: [ OK ] Simd4FloatingpointTest.set (0 ms) 27: [ RUN ] Simd4FloatingpointTest.add 27: [ OK ] Simd4FloatingpointTest.add (0 ms) 27: [ RUN ] Simd4FloatingpointTest.sub 27: [ OK ] Simd4FloatingpointTest.sub (0 ms) 27: [ RUN ] Simd4FloatingpointTest.mul 27: [ OK ] Simd4FloatingpointTest.mul (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fma 27: [ OK ] Simd4FloatingpointTest.fma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fms 27: [ OK ] Simd4FloatingpointTest.fms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnma 27: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnms 27: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.abs 27: [ OK ] Simd4FloatingpointTest.abs (0 ms) 27: [ RUN ] Simd4FloatingpointTest.neg 27: [ OK ] Simd4FloatingpointTest.neg (0 ms) 27: [ RUN ] Simd4FloatingpointTest.and 27: [ OK ] Simd4FloatingpointTest.and (0 ms) 27: [ RUN ] Simd4FloatingpointTest.or 27: [ OK ] Simd4FloatingpointTest.or (0 ms) 27: [ RUN ] Simd4FloatingpointTest.xor 27: [ OK ] Simd4FloatingpointTest.xor (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andNot 27: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 27: [ RUN ] Simd4FloatingpointTest.max 27: [ OK ] Simd4FloatingpointTest.max (0 ms) 27: [ RUN ] Simd4FloatingpointTest.min 27: [ OK ] Simd4FloatingpointTest.min (0 ms) 27: [ RUN ] Simd4FloatingpointTest.round 27: [ OK ] Simd4FloatingpointTest.round (0 ms) 27: [ RUN ] Simd4FloatingpointTest.trunc 27: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 27: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 27: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.selectByNotMask 27: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpNe 27: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLe 27: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLt 27: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andB 27: [ OK ] Simd4FloatingpointTest.andB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.orB 27: [ OK ] Simd4FloatingpointTest.orB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.anyTrue 27: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 27: [ RUN ] Simd4FloatingpointTest.blend 27: [ OK ] Simd4FloatingpointTest.blend (0 ms) 27: [ RUN ] Simd4FloatingpointTest.reduce 27: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 27: [ RUN ] Simd4FloatingpointTest.dotProduct 27: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 27: [ RUN ] Simd4FloatingpointTest.transpose 27: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 27: [----------] 32 tests from Simd4FloatingpointTest (1 ms total) 27: 27: [----------] 1 test from Simd4VectorOperationsTest 27: [ RUN ] Simd4VectorOperationsTest.norm2 27: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 27: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 27: 27: [----------] 2 tests from Simd4MathTest 27: [ RUN ] Simd4MathTest.invsqrt 27: [ OK ] Simd4MathTest.invsqrt (0 ms) 27: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 27: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 27: [----------] 2 tests from Simd4MathTest (0 ms total) 27: 27: [----------] 41 tests from SimdScalarTest 27: [ RUN ] SimdScalarTest.load 27: [ OK ] SimdScalarTest.load (0 ms) 27: [ RUN ] SimdScalarTest.loadU 27: [ OK ] SimdScalarTest.loadU (0 ms) 27: [ RUN ] SimdScalarTest.store 27: [ OK ] SimdScalarTest.store (0 ms) 27: [ RUN ] SimdScalarTest.storeU 27: [ OK ] SimdScalarTest.storeU (0 ms) 27: [ RUN ] SimdScalarTest.setZero 27: [ OK ] SimdScalarTest.setZero (0 ms) 27: [ RUN ] SimdScalarTest.andNot 27: [ OK ] SimdScalarTest.andNot (0 ms) 27: [ RUN ] SimdScalarTest.fma 27: [ OK ] SimdScalarTest.fma (0 ms) 27: [ RUN ] SimdScalarTest.fms 27: [ OK ] SimdScalarTest.fms (0 ms) 27: [ RUN ] SimdScalarTest.fnma 27: [ OK ] SimdScalarTest.fnma (0 ms) 27: [ RUN ] SimdScalarTest.fnms 27: [ OK ] SimdScalarTest.fnms (0 ms) 27: [ RUN ] SimdScalarTest.maskAdd 27: [ OK ] SimdScalarTest.maskAdd (0 ms) 27: [ RUN ] SimdScalarTest.maskzMul 27: [ OK ] SimdScalarTest.maskzMul (0 ms) 27: [ RUN ] SimdScalarTest.maskzFma 27: [ OK ] SimdScalarTest.maskzFma (0 ms) 27: [ RUN ] SimdScalarTest.abs 27: [ OK ] SimdScalarTest.abs (0 ms) 27: [ RUN ] SimdScalarTest.max 27: [ OK ] SimdScalarTest.max (0 ms) 27: [ RUN ] SimdScalarTest.min 27: [ OK ] SimdScalarTest.min (0 ms) 27: [ RUN ] SimdScalarTest.round 27: [ OK ] SimdScalarTest.round (0 ms) 27: [ RUN ] SimdScalarTest.trunc 27: [ OK ] SimdScalarTest.trunc (0 ms) 27: [ RUN ] SimdScalarTest.reduce 27: [ OK ] SimdScalarTest.reduce (0 ms) 27: [ RUN ] SimdScalarTest.testBits 27: [ OK ] SimdScalarTest.testBits (0 ms) 27: [ RUN ] SimdScalarTest.anyTrue 27: [ OK ] SimdScalarTest.anyTrue (0 ms) 27: [ RUN ] SimdScalarTest.selectByMask 27: [ OK ] SimdScalarTest.selectByMask (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMask 27: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 27: [ RUN ] SimdScalarTest.blend 27: [ OK ] SimdScalarTest.blend (0 ms) 27: [ RUN ] SimdScalarTest.cvtR2I 27: [ OK ] SimdScalarTest.cvtR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvttR2I 27: [ OK ] SimdScalarTest.cvttR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvtI2R 27: [ OK ] SimdScalarTest.cvtI2R (0 ms) 27: [ RUN ] SimdScalarTest.cvtF2D 27: [ OK ] SimdScalarTest.cvtF2D (0 ms) 27: [ RUN ] SimdScalarTest.cvtD2D 27: [ OK ] SimdScalarTest.cvtD2D (0 ms) 27: [ RUN ] SimdScalarTest.loadI 27: [ OK ] SimdScalarTest.loadI (0 ms) 27: [ RUN ] SimdScalarTest.loadUI 27: [ OK ] SimdScalarTest.loadUI (0 ms) 27: [ RUN ] SimdScalarTest.storeI 27: [ OK ] SimdScalarTest.storeI (0 ms) 27: [ RUN ] SimdScalarTest.storeUI 27: [ OK ] SimdScalarTest.storeUI (0 ms) 27: [ RUN ] SimdScalarTest.andNotI 27: [ OK ] SimdScalarTest.andNotI (0 ms) 27: [ RUN ] SimdScalarTest.testBitsI 27: [ OK ] SimdScalarTest.testBitsI (0 ms) 27: [ RUN ] SimdScalarTest.selectByMaskI 27: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMaskI 27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 27: [ RUN ] SimdScalarTest.blendI 27: [ OK ] SimdScalarTest.blendI (0 ms) 27: [ RUN ] SimdScalarTest.cvtB2IB 27: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 27: [ RUN ] SimdScalarTest.cvtIB2B 27: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 27: [ RUN ] SimdScalarTest.expandScalarsToTriplets 27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 27: [----------] 41 tests from SimdScalarTest (0 ms total) 27: 27: [----------] 8 tests from SimdScalarUtilTest 27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 27: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 27: 27: [----------] 37 tests from SimdScalarMathTest 27: [ RUN ] SimdScalarMathTest.copysign 27: [ OK ] SimdScalarMathTest.copysign (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPair 27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdScalarMathTest.inv 27: [ OK ] SimdScalarMathTest.inv (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrt 27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdScalarMathTest.log 27: [ OK ] SimdScalarMathTest.log (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2 27: [ OK ] SimdScalarMathTest.exp2 (0 ms) 27: [ RUN ] SimdScalarMathTest.exp 27: [ OK ] SimdScalarMathTest.exp (0 ms) 27: [ RUN ] SimdScalarMathTest.erf 27: [ OK ] SimdScalarMathTest.erf (0 ms) 27: [ RUN ] SimdScalarMathTest.erfc 27: [ OK ] SimdScalarMathTest.erfc (0 ms) 27: [ RUN ] SimdScalarMathTest.sincos 27: [ OK ] SimdScalarMathTest.sincos (0 ms) 27: [ RUN ] SimdScalarMathTest.sin 27: [ OK ] SimdScalarMathTest.sin (0 ms) 27: [ RUN ] SimdScalarMathTest.cos 27: [ OK ] SimdScalarMathTest.cos (0 ms) 27: [ RUN ] SimdScalarMathTest.tan 27: [ OK ] SimdScalarMathTest.tan (0 ms) 27: [ RUN ] SimdScalarMathTest.asin 27: [ OK ] SimdScalarMathTest.asin (0 ms) 27: [ RUN ] SimdScalarMathTest.acos 27: [ OK ] SimdScalarMathTest.acos (0 ms) 27: [ RUN ] SimdScalarMathTest.atan 27: [ OK ] SimdScalarMathTest.atan (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2 27: [ OK ] SimdScalarMathTest.atan2 (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrection 27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.invSingleAccuracy 27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.logSingleAccuracy 27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.expSingleAccuracy 27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 27: [----------] 37 tests from SimdScalarMathTest (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 288 tests from 22 test cases ran. (108 ms total) 27: [ PASSED ] 288 tests. 27/54 Test #27: SimdUnitTests ....................... Passed 0.14 sec test 28 Start 28: CompatibilityHelpersTests 28: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 28: Test timeout computed to be: 30 28: [==========] Running 170 tests from 12 test cases. 28: [----------] Global test environment set-up. 28: [----------] 45 tests from OptionalTest 28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes 28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructEmpty 28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms) 28: [ RUN ] OptionalTest.CanConstructFromNullopt 28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType 28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral 28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting 28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValue 28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting 28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValue 28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral 28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage 28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral 28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromValue 28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignFromValue 28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanResetContent 28: [ OK ] OptionalTest.CanResetContent (0 ms) 28: [ RUN ] OptionalTest.ProvidesRelationalOperators 28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators 28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.CanProduceHash 28: [ OK ] OptionalTest.CanProduceHash (0 ms) 28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType 28: alignment_of: 1 28: alignment_of: 2 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 16 28: alignment_of: 1 28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms) 28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType 28: sizeof( nonstd::optional_lite::detail::storage_t ): 1 28: sizeof( optional ): 2 (1) 28: sizeof( optional ): 4 (2) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 32 (16) 28: sizeof( optional ): 2 (1) 28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms) 28: [----------] 45 tests from OptionalTest (0 ms total) 28: 28: [----------] 7 tests from MakeOptionalTest 28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] MakeOptionalTest.CanCopyConstruct 28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanMoveConstruct 28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms) 28: [----------] 7 tests from MakeOptionalTest (0 ms total) 28: 28: [----------] 4 tests from OptionalMemberSwapTest 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms) 28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total) 28: 28: [----------] 4 tests from OptionalImplicitValueTest 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms) 28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total) 28: 28: [----------] 20 tests from OptionalIntValueTest 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool 28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms) 28: [----------] 20 tests from OptionalIntValueTest (0 ms total) 28: 28: [----------] 1 test from NotNullConstruction 28: [ RUN ] NotNullConstruction.Works 28: [ OK ] NotNullConstruction.Works (0 ms) 28: [----------] 1 test from NotNullConstruction (0 ms total) 28: 28: [----------] 1 test from NotNullCasting 28: [ RUN ] NotNullCasting.Works 28: [ OK ] NotNullCasting.Works (0 ms) 28: [----------] 1 test from NotNullCasting (0 ms total) 28: 28: [----------] 1 test from NotNullAssignment 28: [ RUN ] NotNullAssignment.Works 28: [ OK ] NotNullAssignment.Works (0 ms) 28: [----------] 1 test from NotNullAssignment (0 ms total) 28: 28: [----------] 1 test from MakeNotNull 28: [ RUN ] MakeNotNull.Works 28: [ OK ] MakeNotNull.Works (0 ms) 28: [----------] 1 test from MakeNotNull (0 ms total) 28: 28: [----------] 1 test from NotNull 28: [ RUN ] NotNull.WorksInContainers 28: [ OK ] NotNull.WorksInContainers (0 ms) 28: [----------] 1 test from NotNull (0 ms total) 28: 28: [----------] 80 tests from StringViewTest 28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView 28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize 28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromCString 28: [ OK ] StringViewTest.CanConstructFromCString (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.AllowForwardIteration 28: [ OK ] StringViewTest.AllowForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstForwardIteration 28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowReverseIteration 28: [ OK ] StringViewTest.AllowReverseIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstReverseIteration 28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms) 28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize 28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms) 28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty 28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex 28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaAt 28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms) 28: [ RUN ] StringViewTest.CanAccessAllElementsViaData 28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms) 28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr 28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms) 28: [ RUN ] StringViewTest.CanRemovePrefix 28: [ OK ] StringViewTest.CanRemovePrefix (0 ms) 28: [ RUN ] StringViewTest.CanRemoveSuffix 28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms) 28: [ RUN ] StringViewTest.CanSwapWithOtherView 28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms) 28: [ RUN ] StringViewTest.CanCopySubstringWithCopy 28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms) 28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr 28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms) 28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare 28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare 28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCompareToViews 28: [ OK ] StringViewTest.CanCompareToViews (0 ms) 28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView 28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms) 28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual 28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms) 28: [ RUN ] StringViewTest.CanPrintViewToPutputStream 28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms) 28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms) 28: [----------] 80 tests from StringViewTest (1 ms total) 28: 28: [----------] 5 tests from StringViewExtensionTest 28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString 28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms) 28: [----------] 5 tests from StringViewExtensionTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 170 tests from 12 test cases ran. (3 ms total) 28: [ PASSED ] 170 tests. 28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.04 sec test 29 Start 29: GmxAnaTest 29: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/GmxAnaTest.xml" 29: Test timeout computed to be: 600 29: [==========] Running 27 tests from 5 test cases. 29: [----------] Global test environment set-up. 29: [----------] 5 tests from Entropy 29: [ RUN ] Entropy.Schlitter_300_NoLinear 29: [ OK ] Entropy.Schlitter_300_NoLinear (1 ms) 29: [ RUN ] Entropy.Schlitter_300_Linear 29: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_200_Linear 29: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 29: [----------] 5 tests from Entropy (1 ms total) 29: 29: [----------] 10 tests from MindistTest 29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (1 ms) 29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 2: 'atom3' 29: Selected 3: 'atoms12' 29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (1 ms) 29: [ RUN ] MindistTest.mindistPicksUpContacts 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistPicksUpContacts (1 ms) 29: [ RUN ] MindistTest.ngWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.ngWorks (0 ms) 29: [ RUN ] MindistTest.groupWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 3: 'atoms12' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.groupWorks (1 ms) 29: [ RUN ] MindistTest.maxDistWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 2: 'atom3' 29: Selected 3: 'atoms12' 29: [ OK ] MindistTest.maxDistWorks (8 ms) 29: [ RUN ] MindistTest.noPbcWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.noPbcWorks (0 ms) 29: [ RUN ] MindistTest.resPerTimeWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 3: 'atoms12' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.resPerTimeWorks (1 ms) 29: [ RUN ] MindistTest.matrixWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 5: 'atoms123' 29: Special case: making distance matrix between all atoms in group atoms123 29: [ OK ] MindistTest.matrixWorks (0 ms) 29: [----------] 10 tests from MindistTest (14 ms total) 29: 29: [----------] 3 tests from MsdTest 29: [ RUN ] MsdTest.threeDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.threeDimensionalDiffusion (1 ms) 29: [ RUN ] MsdTest.twoDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.twoDimensionalDiffusion (1 ms) 29: [ RUN ] MsdTest.oneDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.oneDimensionalDiffusion (0 ms) 29: [----------] 3 tests from MsdTest (2 ms total) 29: 29: [----------] 3 tests from MsdMolTest 29: [ RUN ] MsdMolTest.diffMolMassWeighted 29: 29: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to 1533534207 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( water) has 15 elements 29: There is one group in the index 29: Split group of 15 atoms into 5 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 6.4731 Std. Dev. = 8.0969 Error = 3.6210 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolMassWeighted (1038 ms) 29: [ RUN ] MsdMolTest.diffMolNonMassWeighted 29: 29: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to 1466629715 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( water) has 15 elements 29: There is one group in the index 29: Split group of 15 atoms into 5 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 6.4731 Std. Dev. = 8.0969 Error = 3.6210 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolNonMassWeighted (949 ms) 29: [ RUN ] MsdMolTest.diffMolSelected 29: 29: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to -41959458 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( mol) has 9 elements 29: There is one group in the index 29: Split group of 9 atoms into 3 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 7.3593 Std. Dev. = 9.7910 Error = 5.6529 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolSelected (476 ms) 29: [----------] 3 tests from MsdMolTest (2463 ms total) 29: 29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: trr version: GMX_trn_file (single precision) 29: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (3 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (2 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frames from gro file '', 6 atoms. 29: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 't= 0.00000', 6 atoms 29: Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (9 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 27 tests from 5 test cases ran. (2489 ms total) 29: [ PASSED ] 27 tests. 29/54 Test #29: GmxAnaTest .......................... Passed 2.53 sec test 30 Start 30: GmxPreprocessTests 30: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 30: Test timeout computed to be: 30 30: [==========] Running 69 tests from 10 test cases. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from GenconfTest 30: [ RUN ] GenconfTest.nbox_Works 30: [ OK ] GenconfTest.nbox_Works (0 ms) 30: [ RUN ] GenconfTest.nbox_norenumber_Works 30: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 30: [ RUN ] GenconfTest.nbox_dist_Works 30: [ OK ] GenconfTest.nbox_dist_Works (1 ms) 30: [ RUN ] GenconfTest.nbox_rot_Works 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 30: [----------] 4 tests from GenconfTest (3 ms total) 30: 30: [----------] 2 tests from GenionTest 30: [ RUN ] GenionTest.HighConcentrationIonPlacement 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 30: buffer. The cluster pair list does have a buffering effect, but choosing 30: a larger rlist might be necessary for good energy conservation. 30: 30: 30: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: Setting the LD random seed to -2797729 30: Generated 331705 of the 331705 non-bonded parameter combinations 30: Generating 1-4 interactions: fudge = 0.5 30: Generated 331705 of the 331705 1-4 parameter combinations 30: Excluding 2 bonded neighbours molecule type 'SOL' 30: Excluding 3 bonded neighbours molecule type 'methane' 30: Number of degrees of freedom in T-Coupling group rest is 1308.00 30: 30: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: You are using a plain Coulomb cut-off, which might produce artifacts. 30: You might want to consider using PME electrostatics. 30: 30: 30: 30: There were 3 notes 30: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 30: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 30: Group 0 ( System) has 653 elements 30: Group 1 ( Water) has 648 elements 30: Group 2 ( SOL) has 648 elements 30: Group 3 ( non-Water) has 5 elements 30: Group 4 ( Other) has 5 elements 30: Group 5 ( METH) has 5 elements 30: Select a group: Number of (3-atomic) solvent molecules: 216 30: Using random seed 1997. 30: Replacing solvent molecule 56 (atom 168) with NA 30: Replacing solvent molecule 120 (atom 360) with NA 30: Replacing solvent molecule 182 (atom 546) with NA 30: Replacing solvent molecule 71 (atom 213) with NA 30: Replacing solvent molecule 189 (atom 567) with CL 30: Replacing solvent molecule 54 (atom 162) with CL 30: Replacing solvent molecule 155 (atom 465) with CL 30: Replacing solvent molecule 99 (atom 297) with CL 30: 30: Analysing residue names: 30: There are: 216 Water residues 30: There are: 1 Other residues 30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 30: This run will generate roughly 0 Mb of data 30: Will try to add 4 NA ions and 4 CL ions. 30: Select a continuous group of solvent molecules 30: Selected 1: 'Water' 30: [ OK ] GenionTest.HighConcentrationIonPlacement (770 ms) 30: [ RUN ] GenionTest.NoIonPlacement 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 30: buffer. The cluster pair list does have a buffering effect, but choosing 30: a larger rlist might be necessary for good energy conservation. 30: 30: 30: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: Setting the LD random seed to -1096055417 30: Generated 331705 of the 331705 non-bonded parameter combinations 30: Generating 1-4 interactions: fudge = 0.5 30: Generated 331705 of the 331705 1-4 parameter combinations 30: Excluding 2 bonded neighbours molecule type 'SOL' 30: Excluding 3 bonded neighbours molecule type 'methane' 30: Number of degrees of freedom in T-Coupling group rest is 1308.00 30: 30: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: You are using a plain Coulomb cut-off, which might produce artifacts. 30: You might want to consider using PME electrostatics. 30: 30: 30: 30: There were 3 notes 30: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 30: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 30: No ions to add, will just copy input configuration. 30: Analysing residue names: 30: There are: 216 Water residues 30: There are: 1 Other residues 30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 30: This run will generate roughly 0 Mb of data 30: [ OK ] GenionTest.NoIonPlacement (472 ms) 30: [----------] 2 tests from GenionTest (1242 ms total) 30: 30: [----------] 1 test from GenRestrTest 30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 30: 30: Reading structure file 30: Group 0 ( System) has 156 elements 30: Group 1 ( Protein) has 156 elements 30: Group 2 ( Protein-H) has 75 elements 30: Group 3 ( C-alpha) has 10 elements 30: Group 4 ( Backbone) has 30 elements 30: Group 5 ( MainChain) has 40 elements 30: Group 6 ( MainChain+Cb) has 49 elements 30: Group 7 ( MainChain+H) has 52 elements 30: Group 8 ( SideChain) has 104 elements 30: Group 9 ( SideChain-H) has 35 elements 30: Select a group: Select group to position restrain 30: Selected 3: 'C-alpha' 30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (3 ms) 30: [----------] 1 test from GenRestrTest (3 ms total) 30: 30: [----------] 9 tests from PreprocessingAtomTypesTest 30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 30: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 30: 30: [----------] 10 tests from PreprocessingBondAtomTypeTest 30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 30: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 30: 30: [----------] 5 tests from InsertMoleculesTest 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 8 atoms)! 30: 30: Added 1 molecules (out of 1 requested) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 30: 30: Output configuration contains 8 atoms in 4 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (2 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 2 atoms)! 30: Try 2 success (now 4 atoms)! 30: Try 3 success (now 6 atoms)! 30: Try 4 success (now 8 atoms)! 30: Try 5 success (now 10 atoms)! 30: 30: Added 5 molecules (out of 5 requested) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 30: 30: Output configuration contains 10 atoms in 10 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 8 atoms)! 30: Try 2 success (now 10 atoms)! 30: 30: Added 2 molecules (out of 2 requested) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 30: 30: Output configuration contains 10 atoms in 4 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 650 atoms)! 30: Try 2 success (now 652 atoms)! 30: Try 3 success (now 654 atoms)! 30: Try 4 success (now 656 atoms)! 30: 30: Added 4 molecules (out of 4 requested) 30: Replaced 8 residues (24 atoms) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 30: 30: Output configuration contains 632 atoms in 212 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (9 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Read 4 positions from file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 30: 30: Try 1 success (now 2 atoms)! 30: Try 2 success (now 4 atoms)! 30: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 30: Try 13 success (now 6 atoms)! 30: 30: Added 3 molecules (out of 4 requested) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 30: 30: Output configuration contains 6 atoms in 3 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (1 ms) 30: [----------] 5 tests from InsertMoleculesTest (14 ms total) 30: 30: [----------] 14 tests from GetIrTest 30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 30: Ignoring obsolete mdp entry 'title' 30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (3 ms) 30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (26 ms) 30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (3 ms) 30: [ RUN ] GetIrTest.RejectsValueWithoutKey 30: [ OK ] GetIrTest.RejectsValueWithoutKey (25 ms) 30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (31 ms) 30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (3 ms) 30: [ RUN ] GetIrTest.AcceptsEmptyLines 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 30: [ RUN ] GetIrTest.AcceptsElectricField 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricField (11 ms) 30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (3 ms) 30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (2 ms) 30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (13 ms) 30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (3 ms) 30: [ RUN ] GetIrTest.RejectsImplicitSolventYes 30: [ OK ] GetIrTest.RejectsImplicitSolventYes (7 ms) 30: [ RUN ] GetIrTest.AcceptsMimic 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsMimic (2 ms) 30: [----------] 14 tests from GetIrTest (134 ms total) 30: 30: [----------] 5 tests from SolvateTest 30: [ RUN ] SolvateTest.cs_box_Works 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 1x1x1 boxes 30: Solvent box contains 270 atoms in 90 residues 30: Removed 129 solvent atoms due to solvent-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 47 residues 30: Generated solvent containing 141 atoms in 47 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 30: 30: Output configuration contains 141 atoms in 47 residues 30: Volume : 1.331 (nm^3) 30: Density : 1056.36 (g/l) 30: Number of solvent molecules: 47 30: 30: [ OK ] SolvateTest.cs_box_Works (12 ms) 30: [ RUN ] SolvateTest.cs_cp_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 886 residues 30: Generated solvent containing 2658 atoms in 886 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 30: 30: Output configuration contains 2664 atoms in 888 residues 30: Volume : 27.2709 (nm^3) 30: Density : 974.777 (g/l) 30: Number of solvent molecules: 886 30: 30: [ OK ] SolvateTest.cs_cp_Works (59 ms) 30: [ RUN ] SolvateTest.cs_cp_p_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 886 residues 30: Generated solvent containing 2658 atoms in 886 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 30: 30: Output configuration contains 2664 atoms in 888 residues 30: Volume : 27.2709 (nm^3) 30: Density : 974.777 (g/l) 30: Number of solvent molecules: 886 30: 30: Processing topology 30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 30: [ OK ] SolvateTest.cs_cp_p_Works (58 ms) 30: [ RUN ] SolvateTest.shell_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 1902 solvent atoms more than 1.000000 nm from solute. 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 252 residues 30: Generated solvent containing 756 atoms in 252 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 30: 30: Output configuration contains 762 atoms in 254 residues 30: Volume : 27.2709 (nm^3) 30: Density : 279.3 (g/l) 30: Number of solvent molecules: 252 30: 30: [ OK ] SolvateTest.shell_Works (26 ms) 30: [ RUN ] SolvateTest.update_Topology_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 3x3x3 boxes 30: Solvent box contains 14952 atoms in 4984 residues 30: Removed 2787 solvent atoms due to solvent-solvent overlap 30: Removed 30 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 2 different molecule types: 30: HOH ( 3 atoms): 1876 residues 30: SOL ( 3 atoms): 2169 residues 30: Generated solvent containing 0 atoms in 0 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 30: 30: Output configuration contains 12141 atoms in 4047 residues 30: Volume : 125 (nm^3) 30: Density : 968.963 (g/l) 30: Number of solvent molecules: 4045 30: 30: Processing topology 30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 30: [ OK ] SolvateTest.update_Topology_Works (225 ms) 30: [----------] 5 tests from SolvateTest (380 ms total) 30: 30: [----------] 1 test from TopDirTests 30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 30: [----------] 1 test from TopDirTests (0 ms total) 30: 30: [----------] 18 tests from SinglePeptideFragments/EditconfTest 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (8 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (6 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (7 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (3 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (3 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (3 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (5 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (3 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (7 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (6 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (5 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (3 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (4 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (3 ms) 30: [----------] 18 tests from SinglePeptideFragments/EditconfTest (74 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 69 tests from 10 test cases ran. (1850 ms total) 30: [ PASSED ] 69 tests. 30/54 Test #30: GmxPreprocessTests .................. Passed 1.87 sec test 31 Start 31: Pdb2gmx1Test 31: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 31: Test timeout computed to be: 30 31: [==========] Running 24 tests from 1 test case. 31: [----------] Global test environment set-up. 31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (105 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (115 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (105 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (94 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (113 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (126 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (120 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (106 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (138 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (128 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (105 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (94 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (111 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (123 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (114 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (102 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (103 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (119 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (106 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (97 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (111 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (123 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (116 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (103 ms) 31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (2677 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 24 tests from 1 test case ran. (2679 ms total) 31: [ PASSED ] 24 tests. 31/54 Test #31: Pdb2gmx1Test ........................ Passed 2.70 sec test 32 Start 32: Pdb2gmx2Test 32: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 32: Test timeout computed to be: 30 32: [==========] Running 32 tests from 2 test cases. 32: [----------] Global test environment set-up. 32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (72 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (77 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (67 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (58 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Marked 37 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 37 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (64 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Marked 53 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 51 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (78 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Marked 36 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 36 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (63 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Marked 33 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 31 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (59 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (60 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (74 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (66 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (65 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Marked 37 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 37 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (76 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Marked 53 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 51 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (136 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Marked 36 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 36 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (118 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Marked 33 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 31 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (96 ms) 32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (1230 ms total) 32: 32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (72 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (84 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (74 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (68 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Marked 39 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 39 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (74 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Marked 57 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 55 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (88 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Marked 38 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 38 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (71 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Marked 35 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 33 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (63 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (65 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (77 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (66 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (65 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Marked 39 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 39 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (70 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Marked 57 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 55 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (80 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Marked 38 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 38 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (70 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Marked 35 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 33 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (65 ms) 32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (1154 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 32 tests from 2 test cases ran. (2385 ms total) 32: [ PASSED ] 32 tests. 32/54 Test #32: Pdb2gmx2Test ........................ Passed 2.40 sec test 33 Start 33: Pdb2gmx3Test 33: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 33: Test timeout computed to be: 30 33: [==========] Running 28 tests from 4 test cases. 33: [----------] Global test environment set-up. 33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 255, now 254 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 691 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 691 dihedrals, 51 impropers, 457 angles 33: 650 pairs, 254 bonds and 0 virtual sites 33: Total mass 1846.132 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (125 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 291, now 290 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 788 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 788 dihedrals, 72 impropers, 516 angles 33: 736 pairs, 290 bonds and 0 virtual sites 33: Total mass 2088.366 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (103 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 262, now 261 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 727 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 727 dihedrals, 56 impropers, 472 angles 33: 667 pairs, 261 bonds and 0 virtual sites 33: Total mass 1861.124 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (90 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 233, now 232 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 634 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 634 dihedrals, 48 impropers, 419 angles 33: 597 pairs, 232 bonds and 0 virtual sites 33: Total mass 1662.888 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (80 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 255, now 254 33: Marked 124 virtual sites 33: Added 16 dummy masses 33: Added 26 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 691 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 691 dihedrals, 51 impropers, 457 angles 33: 650 pairs, 254 bonds and 130 virtual sites 33: Total mass 1846.132 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (97 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 291, now 290 33: Marked 132 virtual sites 33: Added 10 dummy masses 33: Added 19 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 788 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 788 dihedrals, 72 impropers, 516 angles 33: 736 pairs, 290 bonds and 133 virtual sites 33: Total mass 2088.366 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (109 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 262, now 261 33: Marked 123 virtual sites 33: Added 22 dummy masses 33: Added 35 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 727 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 727 dihedrals, 56 impropers, 472 angles 33: 667 pairs, 261 bonds and 132 virtual sites 33: Total mass 1861.124 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (101 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 233, now 232 33: Marked 111 virtual sites 33: Added 18 dummy masses 33: Added 31 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 634 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 634 dihedrals, 48 impropers, 419 angles 33: 597 pairs, 232 bonds and 116 virtual sites 33: Total mass 1662.888 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (87 ms) 33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (793 ms total) 33: 33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 254, now 254 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 663 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 663 dihedrals, 48 impropers, 457 angles 33: 650 pairs, 254 bonds and 0 virtual sites 33: Total mass 1846.115 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (93 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 290, now 290 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 778 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 778 dihedrals, 49 impropers, 516 angles 33: 736 pairs, 290 bonds and 0 virtual sites 33: Total mass 2088.361 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus PHE-33: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (105 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 261, now 261 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 696 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 696 dihedrals, 39 impropers, 472 angles 33: 667 pairs, 261 bonds and 0 virtual sites 33: Total mass 1861.130 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Start terminus ALA-34: NH3+ 33: End terminus ALA-49: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (94 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 232, now 232 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 618 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 618 dihedrals, 38 impropers, 419 angles 33: 597 pairs, 232 bonds and 0 virtual sites 33: Total mass 1662.885 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Start terminus LYS-50: NH3+ 33: End terminus PRO-65: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (83 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 254, now 254 33: Marked 124 virtual sites 33: Added 16 dummy masses 33: Added 26 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 663 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 663 dihedrals, 48 impropers, 457 angles 33: 650 pairs, 254 bonds and 130 virtual sites 33: Total mass 1846.115 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (100 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 290, now 290 33: Marked 132 virtual sites 33: Added 10 dummy masses 33: Added 19 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 778 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 778 dihedrals, 49 impropers, 516 angles 33: 736 pairs, 290 bonds and 133 virtual sites 33: Total mass 2088.361 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus PHE-33: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (111 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 261, now 261 33: Marked 123 virtual sites 33: Added 22 dummy masses 33: Added 35 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 696 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 696 dihedrals, 39 impropers, 472 angles 33: 667 pairs, 261 bonds and 132 virtual sites 33: Total mass 1861.130 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Start terminus ALA-34: NH3+ 33: End terminus ALA-49: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (104 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 232, now 232 33: Marked 111 virtual sites 33: Added 18 dummy masses 33: Added 31 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 618 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 618 dihedrals, 38 impropers, 419 angles 33: 597 pairs, 232 bonds and 116 virtual sites 33: Total mass 1662.885 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Start terminus LYS-50: NH3+ 33: End terminus PRO-65: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (90 ms) 33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (782 ms total) 33: 33: [----------] 8 tests from ChainSep/Pdb2gmxTest 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 258, now 258 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 651 pairs 33: Before cleaning: 661 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 10 cmap torsion pairs 33: There are 661 dihedrals, 46 impropers, 463 angles 33: 648 pairs, 258 bonds and 0 virtual sites 33: Total mass 1882.146 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: 33: Merged chains into joint molecule definitions at 2 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Identified residue PHE6 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Start terminus PHE-6: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 258 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (93 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 50, now 50 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 123 pairs 33: Before cleaning: 123 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 123 dihedrals, 9 impropers, 88 angles 33: 123 pairs, 50 bonds and 0 virtual sites 33: Total mass 434.421 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 10 donors and 7 acceptors were found. 33: There are 7 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS8 33: NE223 33: MET12 SD55 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 125, now 125 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 317 pairs 33: Before cleaning: 322 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 5 cmap torsion pairs 33: There are 322 dihedrals, 19 impropers, 227 angles 33: 314 pairs, 125 bonds and 0 virtual sites 33: Total mass 846.083 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 258 atoms and 16 residues 33: Total mass in system 1882.146 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 4 28 33: 2 'B' 7 58 33: 3 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (28 atoms, 4 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 51 atoms 33: Chain time... 33: Processing chain 2 'B' (58 atoms, 7 residues) 33: Identified residue PHE6 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus PHE-6: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 7 residues with 124 atoms 33: Chain time... 33: Processing chain 3 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 51 atoms 4 residues 33: Including chain 2 in system: 124 atoms 7 residues 33: Including chain 3 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (61 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 258, now 258 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 651 pairs 33: Before cleaning: 661 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 10 cmap torsion pairs 33: There are 661 dihedrals, 46 impropers, 463 angles 33: 648 pairs, 258 bonds and 0 virtual sites 33: Total mass 1882.146 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: 33: Merged chains into joint molecule definitions at 2 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ILE-9: COO- 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 258 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (93 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 10 donors and 12 acceptors were found. 33: There are 13 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 33: SG9 33: HIS8 NE251 1.055 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 115, now 115 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 288 pairs 33: Before cleaning: 293 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 6 cmap torsion pairs 33: There are 293 dihedrals, 23 impropers, 203 angles 33: 285 pairs, 115 bonds and 0 virtual sites 33: Total mass 888.952 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 60, now 60 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 152 pairs 33: Before cleaning: 152 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 152 dihedrals, 5 impropers, 112 angles 33: 152 pairs, 60 bonds and 0 virtual sites 33: Total mass 391.552 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 258 atoms and 16 residues 33: Total mass in system 1882.146 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 8 61 33: 2 'B' 3 25 33: 3 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (61 atoms, 8 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ILE-9: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 8 residues with 114 atoms 33: Chain time... 33: Processing chain 2 'B' (25 atoms, 3 residues) 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 61 atoms 33: Chain time... 33: Processing chain 3 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 114 atoms 8 residues 33: Including chain 2 in system: 61 atoms 3 residues 33: Including chain 3 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (61 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 260, now 260 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 650 pairs 33: Before cleaning: 660 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 8 cmap torsion pairs 33: There are 660 dihedrals, 45 impropers, 466 angles 33: 647 pairs, 260 bonds and 0 virtual sites 33: Total mass 1900.162 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: 33: Merged chains into joint molecule definitions at 3 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Identified residue PHE6 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Start terminus PHE-6: NH3+ 33: End terminus ILE-9: COO- 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 261 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (94 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 50, now 50 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 123 pairs 33: Before cleaning: 123 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 123 dihedrals, 9 impropers, 88 angles 33: 123 pairs, 50 bonds and 0 virtual sites 33: Total mass 434.421 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 6 donors and 4 acceptors were found. 33: There are 3 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 67, now 67 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 164 pairs 33: Before cleaning: 169 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 169 dihedrals, 13 impropers, 118 angles 33: 161 pairs, 67 bonds and 0 virtual sites 33: Total mass 472.547 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 60, now 60 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 152 pairs 33: Before cleaning: 152 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 152 dihedrals, 5 impropers, 112 angles 33: 152 pairs, 60 bonds and 0 virtual sites 33: Total mass 391.552 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 261 atoms and 16 residues 33: Total mass in system 1900.162 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: WARNING: Chain identifier 'B' is used in two non-sequential blocks. 33: They will be treated as separate chains unless you reorder your file. 33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 4 28 33: 2 'B' 4 33 33: 3 'B' 3 25 33: 4 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (28 atoms, 4 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 51 atoms 33: Chain time... 33: Processing chain 2 'B' (33 atoms, 4 residues) 33: Identified residue PHE6 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Start terminus PHE-6: NH3+ 33: End terminus ILE-9: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 66 atoms 33: Chain time... 33: Processing chain 3 'B' (25 atoms, 3 residues) 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 61 atoms 33: Chain time... 33: Processing chain 4 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 51 atoms 4 residues 33: Including chain 2 in system: 66 atoms 4 residues 33: Including chain 3 in system: 61 atoms 3 residues 33: Including chain 4 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (59 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 256, now 256 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 652 pairs 33: Before cleaning: 662 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 12 cmap torsion pairs 33: There are 662 dihedrals, 47 impropers, 460 angles 33: 649 pairs, 256 bonds and 0 virtual sites 33: Total mass 1864.131 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: 33: Merged chains into joint molecule definitions at 1 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (92 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 14 donors and 15 acceptors were found. 33: There are 20 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 173, now 173 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 441 pairs 33: Before cleaning: 446 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 9 cmap torsion pairs 33: There are 446 dihedrals, 29 impropers, 312 angles 33: 438 pairs, 173 bonds and 0 virtual sites 33: Total mass 1262.488 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 255 atoms and 16 residues 33: Total mass in system 1864.131 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 11 86 33: 2 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (86 atoms, 11 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 11 residues with 172 atoms 33: Chain time... 33: Processing chain 2 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 172 atoms 11 residues 33: Including chain 2 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (69 ms) 33: [----------] 8 tests from ChainSep/Pdb2gmxTest (622 ms total) 33: 33: [----------] 4 tests from ChainChanges/Pdb2gmxTest 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (42 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (43 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (43 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (43 ms) 33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (171 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 28 tests from 4 test cases ran. (2368 ms total) 33: [ PASSED ] 28 tests. 33/54 Test #33: Pdb2gmx3Test ........................ Passed 2.41 sec test 34 Start 34: CorrelationsTest 34: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/CorrelationsTest.xml" 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 3 test cases. 34: [----------] Global test environment set-up. 34: [----------] 10 tests from AutocorrTest 34: [ RUN ] AutocorrTest.EacNormal 34: [ OK ] AutocorrTest.EacNormal (143 ms) 34: [ RUN ] AutocorrTest.EacNoNormalize 34: [ OK ] AutocorrTest.EacNoNormalize (57 ms) 34: [ RUN ] AutocorrTest.EacCos 34: [ OK ] AutocorrTest.EacCos (139 ms) 34: [ RUN ] AutocorrTest.EacVector 34: [ OK ] AutocorrTest.EacVector (208 ms) 34: [ RUN ] AutocorrTest.EacRcross 34: [ OK ] AutocorrTest.EacRcross (1 ms) 34: [ RUN ] AutocorrTest.EacP0 34: [ OK ] AutocorrTest.EacP0 (204 ms) 34: [ RUN ] AutocorrTest.EacP1 34: [ OK ] AutocorrTest.EacP1 (207 ms) 34: [ RUN ] AutocorrTest.EacP2 34: [ OK ] AutocorrTest.EacP2 (418 ms) 34: [ RUN ] AutocorrTest.EacP3 34: [ OK ] AutocorrTest.EacP3 (12 ms) 34: [ RUN ] AutocorrTest.EacP4 34: [ OK ] AutocorrTest.EacP4 (207 ms) 34: [----------] 10 tests from AutocorrTest (1596 ms total) 34: 34: [----------] 1 test from ManyAutocorrelationTest 34: [ RUN ] ManyAutocorrelationTest.Empty 34: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 34: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 34: 34: [----------] 10 tests from ExpfitTest 34: [ RUN ] ExpfitTest.EffnEXP1 34: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 34: [ RUN ] ExpfitTest.EffnEXP2 34: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 34: [ RUN ] ExpfitTest.EffnEXPEXP 34: [ OK ] ExpfitTest.EffnEXPEXP (10 ms) 34: [ RUN ] ExpfitTest.EffnEXP5 34: [ OK ] ExpfitTest.EffnEXP5 (13 ms) 34: [ RUN ] ExpfitTest.EffnEXP7 34: [ OK ] ExpfitTest.EffnEXP7 (11 ms) 34: [ RUN ] ExpfitTest.EffnEXP9 34: [ OK ] ExpfitTest.EffnEXP9 (30 ms) 34: [ RUN ] ExpfitTest.EffnERF 34: [ OK ] ExpfitTest.EffnERF (2 ms) 34: [ RUN ] ExpfitTest.EffnERREST 34: [ OK ] ExpfitTest.EffnERREST (1 ms) 34: [ RUN ] ExpfitTest.EffnVAC 34: [ OK ] ExpfitTest.EffnVAC (7 ms) 34: [ RUN ] ExpfitTest.EffnPRES 34: [ OK ] ExpfitTest.EffnPRES (20 ms) 34: [----------] 10 tests from ExpfitTest (95 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 3 test cases ran. (1705 ms total) 34: [ PASSED ] 21 tests. 34/54 Test #34: CorrelationsTest .................... Passed 1.73 sec test 35 Start 35: AnalysisDataUnitTests 35: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 35: Test timeout computed to be: 30 35: [==========] Running 69 tests from 14 test cases. 35: [----------] Global test environment set-up. 35: [----------] 3 tests from AnalysisDataInitializationTest 35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (1 ms) 35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 35: [----------] 3 tests from AnalysisDataInitializationTest (1 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/0 (3 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/1 (7 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (5 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/2 (9 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/3 (4 ms total) 35: 35: [----------] 4 tests from AnalysisArrayDataTest 35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 35: [ RUN ] AnalysisArrayDataTest.StorageWorks 35: [ OK ] AnalysisArrayDataTest.StorageWorks (1 ms) 35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 35: [----------] 4 tests from AnalysisArrayDataTest (9 ms total) 35: 35: [----------] 6 tests from AverageModuleTest 35: [ RUN ] AverageModuleTest.BasicTest 35: [ OK ] AverageModuleTest.BasicTest (0 ms) 35: [ RUN ] AverageModuleTest.HandlesMultipointData 35: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (1 ms) 35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (1 ms) 35: [ RUN ] AverageModuleTest.CanCustomizeXAxis 35: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 35: [----------] 6 tests from AverageModuleTest (4 ms total) 35: 35: [----------] 2 tests from FrameAverageModuleTest 35: [ RUN ] FrameAverageModuleTest.BasicTest 35: [ OK ] FrameAverageModuleTest.BasicTest (1 ms) 35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 35: [----------] 2 tests from FrameAverageModuleTest (2 ms total) 35: 35: [----------] 7 tests from AnalysisHistogramSettingsTest 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 35: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 35: 35: [----------] 2 tests from SimpleHistogramModuleTest 35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (5 ms) 35: [----------] 2 tests from SimpleHistogramModuleTest (6 ms total) 35: 35: [----------] 3 tests from WeightedHistogramModuleTest 35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) 35: [----------] 3 tests from WeightedHistogramModuleTest (3 ms total) 35: 35: [----------] 3 tests from BinAverageModuleTest 35: [ RUN ] BinAverageModuleTest.ComputesCorrectly 35: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (1 ms) 35: [----------] 3 tests from BinAverageModuleTest (3 ms total) 35: 35: [----------] 4 tests from AbstractAverageHistogramTest 35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (1 ms) 35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (9 ms) 35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) 35: [----------] 4 tests from AbstractAverageHistogramTest (12 ms total) 35: 35: [----------] 3 tests from LifetimeModuleTest 35: [ RUN ] LifetimeModuleTest.BasicTest 35: [ OK ] LifetimeModuleTest.BasicTest (1 ms) 35: [ RUN ] LifetimeModuleTest.CumulativeTest 35: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 35: [----------] 3 tests from LifetimeModuleTest (2 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 69 tests from 14 test cases ran. (65 ms total) 35: [ PASSED ] 69 tests. 35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.10 sec test 36 Start 36: CoordinateIOTests 36: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/CoordinateIOTests.xml" 36: Test timeout computed to be: 30 36: [==========] Running 64 tests from 19 test cases. 36: [----------] Global test environment set-up. 36: [----------] 1 test from OutputSelectorDeathTest 36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (20 ms) 36: [----------] 1 test from OutputSelectorDeathTest (20 ms total) 36: 36: [----------] 5 tests from TrajectoryFrameWriterTest 36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (4 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (8 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (9 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (16 ms) 36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 36: [----------] 5 tests from TrajectoryFrameWriterTest (37 ms total) 36: 36: [----------] 5 tests from OutputAdapterContainer 36: [ RUN ] OutputAdapterContainer.MakeEmpty 36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 36: [ RUN ] OutputAdapterContainer.AddAdapter 36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.RejectBadAdapter 36: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (1 ms) 36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 36: [----------] 5 tests from OutputAdapterContainer (1 ms total) 36: 36: [----------] 5 tests from FlagTest 36: [ RUN ] FlagTest.CanSetSimpleFlag 36: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 36: [ RUN ] FlagTest.CanAddNewBox 36: [ OK ] FlagTest.CanAddNewBox (0 ms) 36: [ RUN ] FlagTest.SetsImplicitPrecisionChange 36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 36: [ RUN ] FlagTest.SetsImplicitStartTimeChange 36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 36: [ RUN ] FlagTest.SetsImplicitTimeStepChange 36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 36: [----------] 5 tests from FlagTest (0 ms total) 36: 36: [----------] 5 tests from SetAtomsTest 36: [ RUN ] SetAtomsTest.RemovesExistingAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.RemovesExistingAtoms (4 ms) 36: [ RUN ] SetAtomsTest.AddsNewAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.AddsNewAtoms (8 ms) 36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (4 ms) 36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (13 ms) 36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (4 ms) 36: [----------] 5 tests from SetAtomsTest (33 ms total) 36: 36: [----------] 2 tests from SetBothTimeTest 36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 36: [----------] 2 tests from SetBothTimeTest (0 ms total) 36: 36: [----------] 2 tests from SetStartTimeTest 36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 36: [ RUN ] SetStartTimeTest.WorksWithZeroStart 36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 36: [----------] 2 tests from SetStartTimeTest (0 ms total) 36: 36: [----------] 1 test from SetTimeStepTest 36: [ RUN ] SetTimeStepTest.SetTimeStepWorks 36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 36: [----------] 1 test from SetTimeStepTest (0 ms total) 36: 36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (12 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (5 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (12 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (4 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (9 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (8 ms) 36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (50 ms total) 36: 36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (4 ms) 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (12 ms) 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (5 ms) 36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (21 ms total) 36: 36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 36: 36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (12 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (17 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (17 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (17 ms) 36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (63 ms total) 36: 36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (8 ms) 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (8 ms) 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (4 ms) 36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (20 ms total) 36: 36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 36: 36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (13 ms) 36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (4 ms) 36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (17 ms total) 36: 36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 36: 36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (5 ms) 36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (5 ms) 36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (10 ms total) 36: 36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (1 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total) 36: 36: [----------] 4 tests from ModuleSupported/NoOptionalOutput 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (4 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (7 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (4 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (4 ms) 36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (19 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 64 tests from 19 test cases ran. (292 ms total) 36: [ PASSED ] 64 tests. 36/54 Test #36: CoordinateIOTests ................... Passed 0.33 sec test 37 Start 37: TrajectoryAnalysisUnitTests 37: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 37: Test timeout computed to be: 30 37: [==========] Running 82 tests from 16 test cases. 37: [----------] Global test environment set-up. 37: [----------] 5 tests from ClustsizeTest 37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 37: There is one group in the index 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 24 37: cmid: 2, cmax: 4, max_size: 6 37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (2 ms) 37: [ RUN ] ClustsizeTest.NoMolShortCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 37: There is one group in the index 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 24 37: cmid: 1, cmax: 6, max_size: 6 37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (1 ms) 37: [ RUN ] ClustsizeTest.MolDefaultCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 2, cmax: 4, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (1 ms) 37: [ RUN ] ClustsizeTest.MolShortCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 1, cmax: 6, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (2 ms) 37: [ RUN ] ClustsizeTest.MolCSize 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 2, cmax: 4, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolCSize (2 ms) 37: [----------] 5 tests from ClustsizeTest (8 ms total) 37: 37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 37: Reading frames from gro file 'Test system', 8 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (3 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 37: Reading frames from gro file 'Test system', 8 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (6 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (10 ms total) 37: 37: [----------] 11 tests from AngleModuleTest 37: [ RUN ] AngleModuleTest.ComputesSimpleAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesSimpleAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesDihedrals 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesDihedrals (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 37: Reading frames from gro file 'Test system for different angles', 33 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesMultipleAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesMultipleAngles (3 ms) 37: [ RUN ] AngleModuleTest.HandlesDynamicSelections 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesDynamicSelections (3 ms) 37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (3 ms) 37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (3 ms) 37: [----------] 11 tests from AngleModuleTest (33 ms total) 37: 37: [----------] 4 tests from ConvertTrjModuleTest 37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (9 ms) 37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (10 ms) 37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (2 ms) 37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 37: [----------] 4 tests from ConvertTrjModuleTest (22 ms total) 37: 37: [----------] 3 tests from DistanceModuleTest 37: [ RUN ] DistanceModuleTest.ComputesDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2: 37: Number of samples: 5 37: Average distance: 1.43246 nm 37: Standard deviation: 0.96700 nm 37: [ OK ] DistanceModuleTest.ComputesDistances (4 ms) 37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2: 37: Number of samples: 5 37: Average distance: 1.43246 nm 37: Standard deviation: 0.96700 nm 37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 37: Number of samples: 4 37: Average distance: 1.81066 nm 37: Standard deviation: 0.79289 nm 37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (4 ms) 37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2 and res_cog x < 2.8: 37: Number of samples: 3 37: Average distance: 1.72076 nm 37: Standard deviation: 1.24839 nm 37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (3 ms) 37: [----------] 3 tests from DistanceModuleTest (11 ms total) 37: 37: [----------] 2 tests from ExtractClusterModuleTest 37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 37: trr version: GMX_trn_file (single precision) 37: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 37: Analyzed 26 frames, last time 0.050 37: There are 8 clusters containing 26 structures, highest framenr is 25 37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (2 ms) 37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 37: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 37: Analyzed 26 frames, last time 0.050 37: There are 8 clusters containing 26 structures, highest framenr is 25 37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 37: [----------] 2 tests from ExtractClusterModuleTest (3 ms total) 37: 37: [----------] 2 tests from FreeVolumeModuleTest 37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for 40 particles. These were set to zero. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: cutoff = 0.18 nm 37: probe_radius = 0 nm 37: seed = 13 37: ninsert = 1000 probes per nm^3 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 37: van der Spoel and Luciano T. Costa 37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Free volume 38.02 +/- 0.00 % 37: Total volume 68.92 +/- 0.00 nm^3 37: Number of molecules 340 total mass 63491.38 Dalton 37: Average molar mass: 186.74 Dalton 37: Density rho: 1529.71 +/- 0.00 nm^3 37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 37: Fractional free volume 0.194 +/- 0.000 37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (106 ms) 37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: cutoff = 0.18 nm 37: probe_radius = 0 nm 37: seed = 17 37: ninsert = 1000 probes per nm^3 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 37: van der Spoel and Luciano T. Costa 37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Free volume 38.48 +/- 0.00 % 37: Total volume 68.92 +/- 0.00 nm^3 37: Number of molecules 340 total mass 63491.38 Dalton 37: Average molar mass: 186.74 Dalton 37: Density rho: 1529.71 +/- 0.00 nm^3 37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 37: Fractional free volume 0.200 +/- 0.000 37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (106 ms) 37: [----------] 2 tests from FreeVolumeModuleTest (212 ms total) 37: 37: [----------] 9 tests from PairDistanceModuleTest 37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (4 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (4 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (4 ms) 37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (3 ms) 37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (3 ms) 37: [----------] 9 tests from PairDistanceModuleTest (30 ms total) 37: 37: [----------] 5 tests from RdfModuleTest 37: [ RUN ] RdfModuleTest.BasicTest 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.BasicTest (28 ms) 37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (17 ms) 37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (27 ms) 37: [ RUN ] RdfModuleTest.CalculatesSurf 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.CalculatesSurf (18 ms) 37: [ RUN ] RdfModuleTest.CalculatesXY 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.CalculatesXY (30 ms) 37: [----------] 5 tests from RdfModuleTest (120 ms total) 37: 37: [----------] 5 tests from SasaModuleTest 37: [ RUN ] SasaModuleTest.BasicTest 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.BasicTest (15 ms) 37: [ RUN ] SasaModuleTest.HandlesSelectedResidues 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesSelectedResidues (9 ms) 37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (9 ms) 37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (12 ms) 37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (11 ms) 37: [----------] 5 tests from SasaModuleTest (56 ms total) 37: 37: [----------] 8 tests from SelectModuleTest 37: [ RUN ] SelectModuleTest.BasicTest 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.BasicTest (6 ms) 37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (5 ms) 37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (4 ms) 37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (5 ms) 37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (4 ms) 37: [ RUN ] SelectModuleTest.NormalizesSizes 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.NormalizesSizes (4 ms) 37: [ RUN ] SelectModuleTest.WritesResidueNumbers 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.WritesResidueNumbers (3 ms) 37: [ RUN ] SelectModuleTest.WritesResidueIndices 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.WritesResidueIndices (3 ms) 37: [----------] 8 tests from SelectModuleTest (34 ms total) 37: 37: [----------] 10 tests from SurfaceAreaTest 37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (1 ms) 37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (1 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints12 37: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints32 37: [ OK ] SurfaceAreaTest.SurfacePoints32 (1 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints42 37: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints122 37: [ OK ] SurfaceAreaTest.SurfacePoints122 (2 ms) 37: [ RUN ] SurfaceAreaTest.Computes100Points 37: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (2 ms) 37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (3 ms) 37: [----------] 10 tests from SurfaceAreaTest (11 ms total) 37: 37: [----------] 4 tests from TopologyInformation 37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 37: [ RUN ] TopologyInformation.WorksWithGroFile 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TopologyInformation.WorksWithGroFile (5 ms) 37: [ RUN ] TopologyInformation.WorksWithPdbFile 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TopologyInformation.WorksWithPdbFile (5 ms) 37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 37: 37: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 2147453862 37: Generated 330891 of the 330891 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 330891 of the 330891 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 37: 37: NOTE 2 [file lysozyme.top, line 1465]: 37: System has non-zero total charge: 2.000000 37: Total charge should normally be an integer. See 37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 37: for discussion on how close it should be to an integer. 37: 37: 37: 37: Number of degrees of freedom in T-Coupling group rest is 465.00 37: 37: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 37: Analysing residue names: 37: There are: 10 Protein residues 37: Analysing Protein... 37: This run will generate roughly 0 Mb of data 37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (627 ms) 37: [----------] 4 tests from TopologyInformation (638 ms total) 37: 37: [----------] 4 tests from TrajectoryModuleTest 37: [ RUN ] TrajectoryModuleTest.BasicTest 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.BasicTest (4 ms) 37: [ RUN ] TrajectoryModuleTest.PlotsXOnly 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.PlotsXOnly (3 ms) 37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (4 ms) 37: [ RUN ] TrajectoryModuleTest.HandlesNoForces 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.HandlesNoForces (3 ms) 37: [----------] 4 tests from TrajectoryModuleTest (14 ms total) 37: 37: [----------] 5 tests from UnionFinderTest 37: [ RUN ] UnionFinderTest.WorksEmpty 37: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 37: [ RUN ] UnionFinderTest.BasicMerges 37: [ OK ] UnionFinderTest.BasicMerges (0 ms) 37: [ RUN ] UnionFinderTest.LargerMerges 37: [ OK ] UnionFinderTest.LargerMerges (0 ms) 37: [ RUN ] UnionFinderTest.LongRightMerge 37: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 37: [ RUN ] UnionFinderTest.LongLeftMerge 37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 37: [----------] 5 tests from UnionFinderTest (0 ms total) 37: 37: [----------] 1 test from MappedUnionFinderTest 37: [ RUN ] MappedUnionFinderTest.BasicMerges 37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 37: [----------] 1 test from MappedUnionFinderTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 82 tests from 16 test cases ran. (1203 ms total) 37: [ PASSED ] 82 tests. 37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 1.22 sec test 38 Start 38: EnergyAnalysisUnitTests 38: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 38: Test timeout computed to be: 30 38: [==========] Running 7 tests from 4 test cases. 38: [----------] Global test environment set-up. 38: [----------] 1 test from DhdlTest 38: [ RUN ] DhdlTest.ExtractDhdl 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 38: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 38: Note: file tpx version 110, software tpx version 119 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 38: 38: 38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 38: [ OK ] DhdlTest.ExtractDhdl (12 ms) 38: [----------] 1 test from DhdlTest (13 ms total) 38: 38: [----------] 1 test from OriresTest 38: [ RUN ] OriresTest.ExtractOrires 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 38: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 38: Note: file tpx version 111, software tpx version 119 38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 38: End your selection with 0 38: Selecting all 7 orientation restraints 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 38: [ OK ] OriresTest.ExtractOrires (18 ms) 38: [----------] 1 test from OriresTest (18 ms total) 38: 38: [----------] 3 tests from EnergyTest 38: [ RUN ] EnergyTest.ExtractEnergy 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 38: [ OK ] EnergyTest.ExtractEnergy (3 ms) 38: [ RUN ] EnergyTest.ExtractEnergyByNumber 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 38: Pres. DC -268.49 3 8.52175 13.2804 (bar) 38: [ OK ] EnergyTest.ExtractEnergyByNumber (11 ms) 38: [ RUN ] EnergyTest.ExtractEnergyMixed 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: [ OK ] EnergyTest.ExtractEnergyMixed (2 ms) 38: [----------] 3 tests from EnergyTest (16 ms total) 38: 38: [----------] 2 tests from ViscosityTest 38: [ RUN ] ViscosityTest.EinsteinViscosity 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Pres-XX 20.2092 65 717.193 185.978 (bar) 38: Pres-XY -47.7351 39 372.522 207.456 (bar) 38: Pres-XZ 11.477 31 379.79 6.80818 (bar) 38: Pres-YX -47.7106 39 372.525 207.5 (bar) 38: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 38: Pres-YZ -41.3534 45 401.216 114.663 (bar) 38: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 38: Pres-ZY -41.3119 45 401.196 114.743 (bar) 38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 38: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: [ OK ] ViscosityTest.EinsteinViscosity (285 ms) 38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Pres-XX 20.2092 65 717.193 185.978 (bar) 38: Pres-XY -47.7351 39 372.522 207.456 (bar) 38: Pres-XZ 11.477 31 379.79 6.80818 (bar) 38: Pres-YX -47.7106 39 372.525 207.5 (bar) 38: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 38: Pres-YZ -41.3534 45 401.216 114.663 (bar) 38: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 38: Pres-ZY -41.3119 45 401.196 114.743 (bar) 38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 38: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (256 ms) 38: [----------] 2 tests from ViscosityTest (541 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 7 tests from 4 test cases ran. (589 ms total) 38: [ PASSED ] 7 tests. 38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 0.63 sec test 39 Start 39: ToolUnitTests 39: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/ToolUnitTests.xml" 39: Test timeout computed to be: 30 39: [==========] Running 18 tests from 4 test cases. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from DumpTest 39: 39: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: For a correct single-point energy evaluation with nsteps = 0, use 39: continuation = yes to avoid constraining the input coordinates. 39: 39: Setting the LD random seed to 2063589359 39: Generated 330891 of the 330891 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 330891 of the 330891 1-4 parameter combinations 39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 39: 39: NOTE 2 [file lysozyme.top, line 1465]: 39: System has non-zero total charge: 2.000000 39: Total charge should normally be an integer. See 39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 39: for discussion on how close it should be to an integer. 39: 39: 39: 39: Number of degrees of freedom in T-Coupling group rest is 465.00 39: 39: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: NVE simulation with an initial temperature of zero: will use a Verlet 39: buffer of 10%. Check your energy drift! 39: 39: 39: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: You are using a plain Coulomb cut-off, which might produce artifacts. 39: You might want to consider using PME electrostatics. 39: 39: 39: 39: There were 4 notes 39: Analysing residue names: 39: There are: 10 Protein residues 39: Analysing Protein... 39: This run will generate roughly 0 Mb of data 39: [ RUN ] DumpTest.WorksWithTpr 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 39: inputrec: 39: integrator = md 39: tinit = 0 39: dt = 0.001 39: nsteps = 0 39: init-step = 0 39: simulation-part = 1 39: comm-mode = Linear 39: nstcomm = 100 39: bd-fric = 0 39: ld-seed = 2063589359 39: emtol = 10 39: emstep = 0.01 39: niter = 20 39: fcstep = 0 39: nstcgsteep = 1000 39: nbfgscorr = 10 39: rtpi = 0.05 39: nstxout = 0 39: nstvout = 0 39: nstfout = 0 39: nstlog = 1000 39: nstcalcenergy = 100 39: nstenergy = 1000 39: nstxout-compressed = 0 39: compressed-x-precision = 1000 39: cutoff-scheme = Verlet 39: nstlist = 10 39: pbc = xyz 39: periodic-molecules = false 39: verlet-buffer-tolerance = -1 39: rlist = 1.1 39: coulombtype = Cut-off 39: coulomb-modifier = Potential-shift 39: rcoulomb-switch = 0 39: rcoulomb = 1 39: epsilon-r = 1 39: epsilon-rf = inf 39: vdw-type = Cut-off 39: vdw-modifier = Potential-shift 39: rvdw-switch = 0 39: rvdw = 1 39: DispCorr = No 39: table-extension = 1 39: fourierspacing = 0.12 39: fourier-nx = 0 39: fourier-ny = 0 39: fourier-nz = 0 39: pme-order = 4 39: ewald-rtol = 1e-05 39: ewald-rtol-lj = 0.001 39: lj-pme-comb-rule = Geometric 39: ewald-geometry = 0 39: epsilon-surface = 0 39: tcoupl = No 39: nsttcouple = -1 39: nh-chain-length = 0 39: print-nose-hoover-chain-variables = false 39: pcoupl = No 39: pcoupltype = Isotropic 39: nstpcouple = -1 39: tau-p = 1 39: compressibility (3x3): 39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p (3x3): 39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: refcoord-scaling = No 39: posres-com (3): 39: posres-com[0]= 0.00000e+00 39: posres-com[1]= 0.00000e+00 39: posres-com[2]= 0.00000e+00 39: posres-comB (3): 39: posres-comB[0]= 0.00000e+00 39: posres-comB[1]= 0.00000e+00 39: posres-comB[2]= 0.00000e+00 39: QMMM = false 39: QMconstraints = 0 39: QMMMscheme = 0 39: MMChargeScaleFactor = 1 39: qm-opts: 39: ngQM = 0 39: constraint-algorithm = Lincs 39: continuation = false 39: Shake-SOR = false 39: shake-tol = 0.0001 39: lincs-order = 4 39: lincs-iter = 1 39: lincs-warnangle = 30 39: nwall = 0 39: wall-type = 9-3 39: wall-r-linpot = -1 39: wall-atomtype[0] = -1 39: wall-atomtype[1] = -1 39: wall-density[0] = 0 39: wall-density[1] = 0 39: wall-ewald-zfac = 3 39: pull = false 39: awh = false 39: rotation = false 39: interactiveMD = false 39: disre = No 39: disre-weighting = Conservative 39: disre-mixed = false 39: dr-fc = 1000 39: dr-tau = 0 39: nstdisreout = 100 39: orire-fc = 0 39: orire-tau = 0 39: nstorireout = 100 39: free-energy = no 39: cos-acceleration = 0 39: deform (3x3): 39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: simulated-tempering = false 39: swapcoords = no 39: userint1 = 0 39: userint2 = 0 39: userint3 = 0 39: userint4 = 0 39: userreal1 = 0 39: userreal2 = 0 39: userreal3 = 0 39: userreal4 = 0 39: applied-forces: 39: electric-field: 39: x: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: y: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: z: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: density-guided-simulation: 39: active = false 39: group = protein 39: similarity-measure = inner-product 39: atom-spreading-weight = unity 39: force-constant = 1e+09 39: gaussian-transform-spreading-width = 0.2 39: gaussian-transform-spreading-range-in-multiples-of-width = 4 39: reference-density-filename = reference.mrc 39: nst = 1 39: normalize-densities = true 39: adaptive-force-scaling = false 39: adaptive-force-scaling-time-constant = 4 39: grpopts: 39: nrdf: 465 39: ref-t: 0 39: tau-t: 0 39: annealing: No 39: annealing-npoints: 0 39: acc: 0 0 0 39: nfreeze: N N N 39: energygrp-flags[ 0]: 0 39: header: 39: bIr = present 39: bBox = present 39: bTop = present 39: bX = present 39: bV = present 39: bF = not present 39: natoms = 156 39: lambda = 0.000000e+00 39: buffer size = 59422 39: topology: 39: name="First 10 residues from 1AKI" 39: #atoms = 156 39: #molblock = 1 39: molblock (0): 39: moltype = 0 "Protein_chain_B" 39: #molecules = 1 39: #posres_xA = 0 39: #posres_xB = 0 39: bIntermolecularInteractions = false 39: ffparams: 39: atnr=10 39: ntypes=212 39: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 39: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 39: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 39: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 39: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 39: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 39: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 39: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 39: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 39: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 39: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 39: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 39: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 39: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 39: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 39: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 39: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 39: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 39: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 39: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 39: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 39: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 39: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 39: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 39: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 39: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 39: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 39: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 39: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 39: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 39: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 39: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 39: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 39: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 39: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 39: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 39: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 39: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 39: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 39: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 39: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 39: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 39: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 39: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 39: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 39: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 39: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 39: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 39: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 39: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 39: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 39: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 39: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 39: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 39: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 39: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 39: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 39: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 39: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 39: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 39: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 39: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 39: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 39: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 39: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 39: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 39: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 39: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 39: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 39: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 39: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 39: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 39: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 39: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 39: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 39: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 39: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 39: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 39: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 39: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 39: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 39: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 39: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 39: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 39: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 39: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 39: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 39: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 39: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 39: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 39: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 39: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 39: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 39: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 39: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 39: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 39: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 39: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 39: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 39: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 39: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 39: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 39: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 39: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 39: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 39: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 39: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 39: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 39: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 39: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 39: reppow = 12 39: fudgeQQ = 0.5 39: cmap 39: atomtypes: 39: atomtype[ 0]={atomnumber= 7} 39: atomtype[ 1]={atomnumber= 1} 39: atomtype[ 2]={atomnumber= 6} 39: atomtype[ 3]={atomnumber= 1} 39: atomtype[ 4]={atomnumber= 6} 39: atomtype[ 5]={atomnumber= 8} 39: atomtype[ 6]={atomnumber= 6} 39: atomtype[ 7]={atomnumber= 1} 39: atomtype[ 8]={atomnumber= 6} 39: atomtype[ 9]={atomnumber= 16} 39: moltype (0): 39: name="Protein_chain_B" 39: atoms: 39: atom (156): 39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 39: atom (156): 39: atom[0]={name="N"} 39: atom[1]={name="H1"} 39: atom[2]={name="H2"} 39: atom[3]={name="H3"} 39: atom[4]={name="CA"} 39: atom[5]={name="HA"} 39: atom[6]={name="CB"} 39: atom[7]={name="HB1"} 39: atom[8]={name="HB2"} 39: atom[9]={name="CG"} 39: atom[10]={name="HG1"} 39: atom[11]={name="HG2"} 39: atom[12]={name="CD"} 39: atom[13]={name="HD1"} 39: atom[14]={name="HD2"} 39: atom[15]={name="CE"} 39: atom[16]={name="HE1"} 39: atom[17]={name="HE2"} 39: atom[18]={name="NZ"} 39: atom[19]={name="HZ1"} 39: atom[20]={name="HZ2"} 39: atom[21]={name="HZ3"} 39: atom[22]={name="C"} 39: atom[23]={name="O"} 39: atom[24]={name="N"} 39: atom[25]={name="H"} 39: atom[26]={name="CA"} 39: atom[27]={name="HA"} 39: atom[28]={name="CB"} 39: atom[29]={name="HB"} 39: atom[30]={name="CG1"} 39: atom[31]={name="HG11"} 39: atom[32]={name="HG12"} 39: atom[33]={name="HG13"} 39: atom[34]={name="CG2"} 39: atom[35]={name="HG21"} 39: atom[36]={name="HG22"} 39: atom[37]={name="HG23"} 39: atom[38]={name="C"} 39: atom[39]={name="O"} 39: atom[40]={name="N"} 39: atom[41]={name="H"} 39: atom[42]={name="CA"} 39: atom[43]={name="HA"} 39: atom[44]={name="CB"} 39: atom[45]={name="HB1"} 39: atom[46]={name="HB2"} 39: atom[47]={name="CG"} 39: atom[48]={name="CD1"} 39: atom[49]={name="HD1"} 39: atom[50]={name="CD2"} 39: atom[51]={name="HD2"} 39: atom[52]={name="CE1"} 39: atom[53]={name="HE1"} 39: atom[54]={name="CE2"} 39: atom[55]={name="HE2"} 39: atom[56]={name="CZ"} 39: atom[57]={name="HZ"} 39: atom[58]={name="C"} 39: atom[59]={name="O"} 39: atom[60]={name="N"} 39: atom[61]={name="H"} 39: atom[62]={name="CA"} 39: atom[63]={name="HA1"} 39: atom[64]={name="HA2"} 39: atom[65]={name="C"} 39: atom[66]={name="O"} 39: atom[67]={name="N"} 39: atom[68]={name="H"} 39: atom[69]={name="CA"} 39: atom[70]={name="HA"} 39: atom[71]={name="CB"} 39: atom[72]={name="HB1"} 39: atom[73]={name="HB2"} 39: atom[74]={name="CG"} 39: atom[75]={name="HG1"} 39: atom[76]={name="HG2"} 39: atom[77]={name="CD"} 39: atom[78]={name="HD1"} 39: atom[79]={name="HD2"} 39: atom[80]={name="NE"} 39: atom[81]={name="HE"} 39: atom[82]={name="CZ"} 39: atom[83]={name="NH1"} 39: atom[84]={name="HH11"} 39: atom[85]={name="HH12"} 39: atom[86]={name="NH2"} 39: atom[87]={name="HH21"} 39: atom[88]={name="HH22"} 39: atom[89]={name="C"} 39: atom[90]={name="O"} 39: atom[91]={name="N"} 39: atom[92]={name="H"} 39: atom[93]={name="CA"} 39: atom[94]={name="HA"} 39: atom[95]={name="CB"} 39: atom[96]={name="HB1"} 39: atom[97]={name="HB2"} 39: atom[98]={name="SG"} 39: atom[99]={name="HG"} 39: atom[100]={name="C"} 39: atom[101]={name="O"} 39: atom[102]={name="N"} 39: atom[103]={name="H"} 39: atom[104]={name="CA"} 39: atom[105]={name="HA"} 39: atom[106]={name="CB"} 39: atom[107]={name="HB1"} 39: atom[108]={name="HB2"} 39: atom[109]={name="CG"} 39: atom[110]={name="HG1"} 39: atom[111]={name="HG2"} 39: atom[112]={name="CD"} 39: atom[113]={name="OE1"} 39: atom[114]={name="OE2"} 39: atom[115]={name="C"} 39: atom[116]={name="O"} 39: atom[117]={name="N"} 39: atom[118]={name="H"} 39: atom[119]={name="CA"} 39: atom[120]={name="HA"} 39: atom[121]={name="CB"} 39: atom[122]={name="HB1"} 39: atom[123]={name="HB2"} 39: atom[124]={name="CG"} 39: atom[125]={name="HG"} 39: atom[126]={name="CD1"} 39: atom[127]={name="HD11"} 39: atom[128]={name="HD12"} 39: atom[129]={name="HD13"} 39: atom[130]={name="CD2"} 39: atom[131]={name="HD21"} 39: atom[132]={name="HD22"} 39: atom[133]={name="HD23"} 39: atom[134]={name="C"} 39: atom[135]={name="O"} 39: atom[136]={name="N"} 39: atom[137]={name="H"} 39: atom[138]={name="CA"} 39: atom[139]={name="HA"} 39: atom[140]={name="CB"} 39: atom[141]={name="HB1"} 39: atom[142]={name="HB2"} 39: atom[143]={name="HB3"} 39: atom[144]={name="C"} 39: atom[145]={name="O"} 39: atom[146]={name="N"} 39: atom[147]={name="H"} 39: atom[148]={name="CA"} 39: atom[149]={name="HA"} 39: atom[150]={name="CB"} 39: atom[151]={name="HB1"} 39: atom[152]={name="HB2"} 39: atom[153]={name="HB3"} 39: atom[154]={name="C"} 39: atom[155]={name="O"} 39: type (156): 39: type[0]={name="opls_287",nameB="opls_287"} 39: type[1]={name="opls_290",nameB="opls_290"} 39: type[2]={name="opls_290",nameB="opls_290"} 39: type[3]={name="opls_290",nameB="opls_290"} 39: type[4]={name="opls_293B",nameB="opls_293B"} 39: type[5]={name="opls_140",nameB="opls_140"} 39: type[6]={name="opls_136",nameB="opls_136"} 39: type[7]={name="opls_140",nameB="opls_140"} 39: type[8]={name="opls_140",nameB="opls_140"} 39: type[9]={name="opls_136",nameB="opls_136"} 39: type[10]={name="opls_140",nameB="opls_140"} 39: type[11]={name="opls_140",nameB="opls_140"} 39: type[12]={name="opls_136",nameB="opls_136"} 39: type[13]={name="opls_140",nameB="opls_140"} 39: type[14]={name="opls_140",nameB="opls_140"} 39: type[15]={name="opls_292",nameB="opls_292"} 39: type[16]={name="opls_140",nameB="opls_140"} 39: type[17]={name="opls_140",nameB="opls_140"} 39: type[18]={name="opls_287",nameB="opls_287"} 39: type[19]={name="opls_290",nameB="opls_290"} 39: type[20]={name="opls_290",nameB="opls_290"} 39: type[21]={name="opls_290",nameB="opls_290"} 39: type[22]={name="opls_235",nameB="opls_235"} 39: type[23]={name="opls_236",nameB="opls_236"} 39: type[24]={name="opls_238",nameB="opls_238"} 39: type[25]={name="opls_241",nameB="opls_241"} 39: type[26]={name="opls_224B",nameB="opls_224B"} 39: type[27]={name="opls_140",nameB="opls_140"} 39: type[28]={name="opls_137",nameB="opls_137"} 39: type[29]={name="opls_140",nameB="opls_140"} 39: type[30]={name="opls_135",nameB="opls_135"} 39: type[31]={name="opls_140",nameB="opls_140"} 39: type[32]={name="opls_140",nameB="opls_140"} 39: type[33]={name="opls_140",nameB="opls_140"} 39: type[34]={name="opls_135",nameB="opls_135"} 39: type[35]={name="opls_140",nameB="opls_140"} 39: type[36]={name="opls_140",nameB="opls_140"} 39: type[37]={name="opls_140",nameB="opls_140"} 39: type[38]={name="opls_235",nameB="opls_235"} 39: type[39]={name="opls_236",nameB="opls_236"} 39: type[40]={name="opls_238",nameB="opls_238"} 39: type[41]={name="opls_241",nameB="opls_241"} 39: type[42]={name="opls_224B",nameB="opls_224B"} 39: type[43]={name="opls_140",nameB="opls_140"} 39: type[44]={name="opls_149",nameB="opls_149"} 39: type[45]={name="opls_140",nameB="opls_140"} 39: type[46]={name="opls_140",nameB="opls_140"} 39: type[47]={name="opls_145",nameB="opls_145"} 39: type[48]={name="opls_145",nameB="opls_145"} 39: type[49]={name="opls_146",nameB="opls_146"} 39: type[50]={name="opls_145",nameB="opls_145"} 39: type[51]={name="opls_146",nameB="opls_146"} 39: type[52]={name="opls_145",nameB="opls_145"} 39: type[53]={name="opls_146",nameB="opls_146"} 39: type[54]={name="opls_145",nameB="opls_145"} 39: type[55]={name="opls_146",nameB="opls_146"} 39: type[56]={name="opls_145",nameB="opls_145"} 39: type[57]={name="opls_146",nameB="opls_146"} 39: type[58]={name="opls_235",nameB="opls_235"} 39: type[59]={name="opls_236",nameB="opls_236"} 39: type[60]={name="opls_238",nameB="opls_238"} 39: type[61]={name="opls_241",nameB="opls_241"} 39: type[62]={name="opls_223B",nameB="opls_223B"} 39: type[63]={name="opls_140",nameB="opls_140"} 39: type[64]={name="opls_140",nameB="opls_140"} 39: type[65]={name="opls_235",nameB="opls_235"} 39: type[66]={name="opls_236",nameB="opls_236"} 39: type[67]={name="opls_238",nameB="opls_238"} 39: type[68]={name="opls_241",nameB="opls_241"} 39: type[69]={name="opls_224B",nameB="opls_224B"} 39: type[70]={name="opls_140",nameB="opls_140"} 39: type[71]={name="opls_136",nameB="opls_136"} 39: type[72]={name="opls_140",nameB="opls_140"} 39: type[73]={name="opls_140",nameB="opls_140"} 39: type[74]={name="opls_308",nameB="opls_308"} 39: type[75]={name="opls_140",nameB="opls_140"} 39: type[76]={name="opls_140",nameB="opls_140"} 39: type[77]={name="opls_307",nameB="opls_307"} 39: type[78]={name="opls_140",nameB="opls_140"} 39: type[79]={name="opls_140",nameB="opls_140"} 39: type[80]={name="opls_303",nameB="opls_303"} 39: type[81]={name="opls_304",nameB="opls_304"} 39: type[82]={name="opls_302",nameB="opls_302"} 39: type[83]={name="opls_300",nameB="opls_300"} 39: type[84]={name="opls_301",nameB="opls_301"} 39: type[85]={name="opls_301",nameB="opls_301"} 39: type[86]={name="opls_300",nameB="opls_300"} 39: type[87]={name="opls_301",nameB="opls_301"} 39: type[88]={name="opls_301",nameB="opls_301"} 39: type[89]={name="opls_235",nameB="opls_235"} 39: type[90]={name="opls_236",nameB="opls_236"} 39: type[91]={name="opls_238",nameB="opls_238"} 39: type[92]={name="opls_241",nameB="opls_241"} 39: type[93]={name="opls_224B",nameB="opls_224B"} 39: type[94]={name="opls_140",nameB="opls_140"} 39: type[95]={name="opls_206",nameB="opls_206"} 39: type[96]={name="opls_140",nameB="opls_140"} 39: type[97]={name="opls_140",nameB="opls_140"} 39: type[98]={name="opls_200",nameB="opls_200"} 39: type[99]={name="opls_204",nameB="opls_204"} 39: type[100]={name="opls_235",nameB="opls_235"} 39: type[101]={name="opls_236",nameB="opls_236"} 39: type[102]={name="opls_238",nameB="opls_238"} 39: type[103]={name="opls_241",nameB="opls_241"} 39: type[104]={name="opls_224B",nameB="opls_224B"} 39: type[105]={name="opls_140",nameB="opls_140"} 39: type[106]={name="opls_136",nameB="opls_136"} 39: type[107]={name="opls_140",nameB="opls_140"} 39: type[108]={name="opls_140",nameB="opls_140"} 39: type[109]={name="opls_274",nameB="opls_274"} 39: type[110]={name="opls_140",nameB="opls_140"} 39: type[111]={name="opls_140",nameB="opls_140"} 39: type[112]={name="opls_271",nameB="opls_271"} 39: type[113]={name="opls_272",nameB="opls_272"} 39: type[114]={name="opls_272",nameB="opls_272"} 39: type[115]={name="opls_235",nameB="opls_235"} 39: type[116]={name="opls_236",nameB="opls_236"} 39: type[117]={name="opls_238",nameB="opls_238"} 39: type[118]={name="opls_241",nameB="opls_241"} 39: type[119]={name="opls_224B",nameB="opls_224B"} 39: type[120]={name="opls_140",nameB="opls_140"} 39: type[121]={name="opls_136",nameB="opls_136"} 39: type[122]={name="opls_140",nameB="opls_140"} 39: type[123]={name="opls_140",nameB="opls_140"} 39: type[124]={name="opls_137",nameB="opls_137"} 39: type[125]={name="opls_140",nameB="opls_140"} 39: type[126]={name="opls_135",nameB="opls_135"} 39: type[127]={name="opls_140",nameB="opls_140"} 39: type[128]={name="opls_140",nameB="opls_140"} 39: type[129]={name="opls_140",nameB="opls_140"} 39: type[130]={name="opls_135",nameB="opls_135"} 39: type[131]={name="opls_140",nameB="opls_140"} 39: type[132]={name="opls_140",nameB="opls_140"} 39: type[133]={name="opls_140",nameB="opls_140"} 39: type[134]={name="opls_235",nameB="opls_235"} 39: type[135]={name="opls_236",nameB="opls_236"} 39: type[136]={name="opls_238",nameB="opls_238"} 39: type[137]={name="opls_241",nameB="opls_241"} 39: type[138]={name="opls_224B",nameB="opls_224B"} 39: type[139]={name="opls_140",nameB="opls_140"} 39: type[140]={name="opls_135",nameB="opls_135"} 39: type[141]={name="opls_140",nameB="opls_140"} 39: type[142]={name="opls_140",nameB="opls_140"} 39: type[143]={name="opls_140",nameB="opls_140"} 39: type[144]={name="opls_235",nameB="opls_235"} 39: type[145]={name="opls_236",nameB="opls_236"} 39: type[146]={name="opls_238",nameB="opls_238"} 39: type[147]={name="opls_241",nameB="opls_241"} 39: type[148]={name="opls_224B",nameB="opls_224B"} 39: type[149]={name="opls_140",nameB="opls_140"} 39: type[150]={name="opls_135",nameB="opls_135"} 39: type[151]={name="opls_140",nameB="opls_140"} 39: type[152]={name="opls_140",nameB="opls_140"} 39: type[153]={name="opls_140",nameB="opls_140"} 39: type[154]={name="opls_235",nameB="opls_235"} 39: type[155]={name="opls_236",nameB="opls_236"} 39: residue (10): 39: residue[0]={name="LYS", nr=1, ic=' '} 39: residue[1]={name="VAL", nr=2, ic=' '} 39: residue[2]={name="PHE", nr=3, ic=' '} 39: residue[3]={name="GLY", nr=4, ic=' '} 39: residue[4]={name="ARG", nr=5, ic=' '} 39: residue[5]={name="CYS", nr=6, ic=' '} 39: residue[6]={name="GLU", nr=7, ic=' '} 39: residue[7]={name="LEU", nr=8, ic=' '} 39: residue[8]={name="ALA", nr=9, ic=' '} 39: residue[9]={name="ALA", nr=10, ic=' '} 39: excls: 39: nr=156 39: nra=1828 39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 39: 23, 24, 25, 26} 39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 39: 14, 15, 22, 23, 24} 39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 39: 16, 17, 18, 22} 39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39: 17, 18, 19, 20, 21} 39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39: 19, 20, 21} 39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 39: 25, 26, 27, 28, 38} 39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26} 39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 39: 30, 34, 38, 39, 40} 39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38} 39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 39: 40} 39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39: 34, 35, 36, 37, 38, 39, 40} 39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 39: 40, 41, 42, 43, 44, 58} 39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42} 39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 39: 45, 46, 47, 58, 59, 60} 39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58} 39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 39: 48, 50, 58, 59, 60, 61, 62} 39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 39: 60} 39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 39: 50, 51, 52, 54, 58, 59, 60} 39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 39: 52, 53, 54, 55, 56, 58} 39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 39: 54, 56, 57} 39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56} 39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 39: 55, 56, 57} 39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56} 39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57} 39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57} 39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57} 39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 39: 60, 61, 62, 63, 64, 65} 39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62} 39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 39: 65, 66, 67} 39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65} 39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 39: 68, 69} 39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67} 39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67} 39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 39: 70, 71, 89} 39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69} 39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 39: 72, 73, 74, 89, 90, 91} 39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89} 39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 39: 75, 76, 77, 89, 90, 91, 92, 93} 39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 39: 91} 39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 39: 77, 78, 79, 80, 89, 90, 91} 39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 39: 79, 80, 81, 82, 89} 39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 39: 81, 82, 83, 86} 39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 39: 84, 85, 86, 87, 88} 39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86} 39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 39: 86, 87, 88} 39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86} 39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86} 39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88} 39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88} 39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 39: 90, 91, 92, 93, 94, 95, 100} 39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93} 39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 39: 95, 96, 97, 98, 100, 101, 102} 39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100} 39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 39: 98, 99, 100, 101, 102, 103, 104} 39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 39: 101, 102} 39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 39: 100, 101, 102} 39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99} 39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 39: 101, 102, 103, 104, 105, 106, 115} 39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104} 39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104, 39: 105, 106, 107, 108, 109, 115, 116, 117} 39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106, 39: 115} 39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106, 39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 115, 116, 117} 39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 110, 111, 112, 113, 114, 115, 116, 117} 39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 115} 39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 115} 39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 113, 114, 115} 39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114} 39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114} 39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 115, 116, 117, 118, 119, 120, 121, 134} 39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118, 39: 119} 39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118, 39: 119, 120, 121, 122, 123, 124, 134, 135, 136} 39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121, 39: 134} 39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121, 39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 134, 135, 136} 39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 39: 136} 39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 130, 134} 39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 130, 134} 39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 127, 128, 129, 130, 131, 132, 133, 134} 39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 134, 135, 136, 137, 138, 139, 140, 144} 39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137, 39: 138} 39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137, 39: 138, 139, 140, 141, 142, 143, 144, 145, 146} 39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140, 39: 144} 39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140, 39: 141, 142, 143, 144, 145, 146, 147, 148} 39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146} 39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146} 39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146, 147, 148, 149, 150, 154} 39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147, 39: 148} 39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147, 39: 148, 149, 150, 151, 152, 153, 154, 155} 39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150, 39: 154} 39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150, 39: 151, 152, 153, 154, 155} 39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155} 39: Bond: 39: nr: 468 39: iatoms: 39: 0 type=100 (BONDS) 0 1 39: 1 type=100 (BONDS) 0 2 39: 2 type=100 (BONDS) 0 3 39: 3 type=101 (BONDS) 0 4 39: 4 type=102 (BONDS) 4 5 39: 5 type=103 (BONDS) 4 6 39: 6 type=104 (BONDS) 4 22 39: 7 type=102 (BONDS) 6 7 39: 8 type=102 (BONDS) 6 8 39: 9 type=103 (BONDS) 6 9 39: 10 type=102 (BONDS) 9 10 39: 11 type=102 (BONDS) 9 11 39: 12 type=103 (BONDS) 9 12 39: 13 type=102 (BONDS) 12 13 39: 14 type=102 (BONDS) 12 14 39: 15 type=103 (BONDS) 12 15 39: 16 type=102 (BONDS) 15 16 39: 17 type=102 (BONDS) 15 17 39: 18 type=101 (BONDS) 15 18 39: 19 type=100 (BONDS) 18 19 39: 20 type=100 (BONDS) 18 20 39: 21 type=100 (BONDS) 18 21 39: 22 type=105 (BONDS) 22 23 39: 23 type=106 (BONDS) 22 24 39: 24 type=100 (BONDS) 24 25 39: 25 type=107 (BONDS) 24 26 39: 26 type=102 (BONDS) 26 27 39: 27 type=103 (BONDS) 26 28 39: 28 type=104 (BONDS) 26 38 39: 29 type=102 (BONDS) 28 29 39: 30 type=103 (BONDS) 28 30 39: 31 type=103 (BONDS) 28 34 39: 32 type=102 (BONDS) 30 31 39: 33 type=102 (BONDS) 30 32 39: 34 type=102 (BONDS) 30 33 39: 35 type=102 (BONDS) 34 35 39: 36 type=102 (BONDS) 34 36 39: 37 type=102 (BONDS) 34 37 39: 38 type=105 (BONDS) 38 39 39: 39 type=106 (BONDS) 38 40 39: 40 type=100 (BONDS) 40 41 39: 41 type=107 (BONDS) 40 42 39: 42 type=102 (BONDS) 42 43 39: 43 type=103 (BONDS) 42 44 39: 44 type=104 (BONDS) 42 58 39: 45 type=102 (BONDS) 44 45 39: 46 type=102 (BONDS) 44 46 39: 47 type=108 (BONDS) 44 47 39: 48 type=109 (BONDS) 47 48 39: 49 type=109 (BONDS) 47 50 39: 50 type=110 (BONDS) 48 49 39: 51 type=109 (BONDS) 48 52 39: 52 type=110 (BONDS) 50 51 39: 53 type=109 (BONDS) 50 54 39: 54 type=110 (BONDS) 52 53 39: 55 type=109 (BONDS) 52 56 39: 56 type=110 (BONDS) 54 55 39: 57 type=109 (BONDS) 54 56 39: 58 type=110 (BONDS) 56 57 39: 59 type=105 (BONDS) 58 59 39: 60 type=106 (BONDS) 58 60 39: 61 type=100 (BONDS) 60 61 39: 62 type=107 (BONDS) 60 62 39: 63 type=102 (BONDS) 62 63 39: 64 type=102 (BONDS) 62 64 39: 65 type=104 (BONDS) 62 65 39: 66 type=105 (BONDS) 65 66 39: 67 type=106 (BONDS) 65 67 39: 68 type=100 (BONDS) 67 68 39: 69 type=107 (BONDS) 67 69 39: 70 type=102 (BONDS) 69 70 39: 71 type=103 (BONDS) 69 71 39: 72 type=104 (BONDS) 69 89 39: 73 type=102 (BONDS) 71 72 39: 74 type=102 (BONDS) 71 73 39: 75 type=103 (BONDS) 71 74 39: 76 type=102 (BONDS) 74 75 39: 77 type=102 (BONDS) 74 76 39: 78 type=103 (BONDS) 74 77 39: 79 type=102 (BONDS) 77 78 39: 80 type=102 (BONDS) 77 79 39: 81 type=111 (BONDS) 77 80 39: 82 type=100 (BONDS) 80 81 39: 83 type=112 (BONDS) 80 82 39: 84 type=112 (BONDS) 82 83 39: 85 type=112 (BONDS) 82 86 39: 86 type=100 (BONDS) 83 84 39: 87 type=100 (BONDS) 83 85 39: 88 type=100 (BONDS) 86 87 39: 89 type=100 (BONDS) 86 88 39: 90 type=105 (BONDS) 89 90 39: 91 type=106 (BONDS) 89 91 39: 92 type=100 (BONDS) 91 92 39: 93 type=107 (BONDS) 91 93 39: 94 type=102 (BONDS) 93 94 39: 95 type=103 (BONDS) 93 95 39: 96 type=104 (BONDS) 93 100 39: 97 type=102 (BONDS) 95 96 39: 98 type=102 (BONDS) 95 97 39: 99 type=113 (BONDS) 95 98 39: 100 type=114 (BONDS) 98 99 39: 101 type=105 (BONDS) 100 101 39: 102 type=106 (BONDS) 100 102 39: 103 type=100 (BONDS) 102 103 39: 104 type=107 (BONDS) 102 104 39: 105 type=102 (BONDS) 104 105 39: 106 type=103 (BONDS) 104 106 39: 107 type=104 (BONDS) 104 115 39: 108 type=102 (BONDS) 106 107 39: 109 type=102 (BONDS) 106 108 39: 110 type=103 (BONDS) 106 109 39: 111 type=102 (BONDS) 109 110 39: 112 type=102 (BONDS) 109 111 39: 113 type=104 (BONDS) 109 112 39: 114 type=115 (BONDS) 112 113 39: 115 type=115 (BONDS) 112 114 39: 116 type=105 (BONDS) 115 116 39: 117 type=106 (BONDS) 115 117 39: 118 type=100 (BONDS) 117 118 39: 119 type=107 (BONDS) 117 119 39: 120 type=102 (BONDS) 119 120 39: 121 type=103 (BONDS) 119 121 39: 122 type=104 (BONDS) 119 134 39: 123 type=102 (BONDS) 121 122 39: 124 type=102 (BONDS) 121 123 39: 125 type=103 (BONDS) 121 124 39: 126 type=102 (BONDS) 124 125 39: 127 type=103 (BONDS) 124 126 39: 128 type=103 (BONDS) 124 130 39: 129 type=102 (BONDS) 126 127 39: 130 type=102 (BONDS) 126 128 39: 131 type=102 (BONDS) 126 129 39: 132 type=102 (BONDS) 130 131 39: 133 type=102 (BONDS) 130 132 39: 134 type=102 (BONDS) 130 133 39: 135 type=105 (BONDS) 134 135 39: 136 type=106 (BONDS) 134 136 39: 137 type=100 (BONDS) 136 137 39: 138 type=107 (BONDS) 136 138 39: 139 type=102 (BONDS) 138 139 39: 140 type=103 (BONDS) 138 140 39: 141 type=104 (BONDS) 138 144 39: 142 type=102 (BONDS) 140 141 39: 143 type=102 (BONDS) 140 142 39: 144 type=102 (BONDS) 140 143 39: 145 type=105 (BONDS) 144 145 39: 146 type=106 (BONDS) 144 146 39: 147 type=100 (BONDS) 146 147 39: 148 type=107 (BONDS) 146 148 39: 149 type=102 (BONDS) 148 149 39: 150 type=103 (BONDS) 148 150 39: 151 type=104 (BONDS) 148 154 39: 152 type=102 (BONDS) 150 151 39: 153 type=102 (BONDS) 150 152 39: 154 type=102 (BONDS) 150 153 39: 155 type=105 (BONDS) 154 155 39: G96Bond: 39: nr: 0 39: Morse: 39: nr: 0 39: Cubic Bonds: 39: nr: 0 39: Connect Bonds: 39: nr: 0 39: Harmonic Pot.: 39: nr: 0 39: FENE Bonds: 39: nr: 0 39: Tab. Bonds: 39: nr: 0 39: Tab. Bonds NC: 39: nr: 0 39: Restraint Pot.: 39: nr: 0 39: Angle: 39: nr: 1124 39: iatoms: 39: 0 type=116 (ANGLES) 1 0 2 39: 1 type=116 (ANGLES) 1 0 3 39: 2 type=116 (ANGLES) 1 0 4 39: 3 type=116 (ANGLES) 2 0 3 39: 4 type=116 (ANGLES) 2 0 4 39: 5 type=116 (ANGLES) 3 0 4 39: 6 type=116 (ANGLES) 0 4 5 39: 7 type=117 (ANGLES) 0 4 6 39: 8 type=117 (ANGLES) 0 4 22 39: 9 type=118 (ANGLES) 5 4 6 39: 10 type=116 (ANGLES) 5 4 22 39: 11 type=119 (ANGLES) 6 4 22 39: 12 type=118 (ANGLES) 4 6 7 39: 13 type=118 (ANGLES) 4 6 8 39: 14 type=120 (ANGLES) 4 6 9 39: 15 type=121 (ANGLES) 7 6 8 39: 16 type=118 (ANGLES) 7 6 9 39: 17 type=118 (ANGLES) 8 6 9 39: 18 type=118 (ANGLES) 6 9 10 39: 19 type=118 (ANGLES) 6 9 11 39: 20 type=120 (ANGLES) 6 9 12 39: 21 type=121 (ANGLES) 10 9 11 39: 22 type=118 (ANGLES) 10 9 12 39: 23 type=118 (ANGLES) 11 9 12 39: 24 type=118 (ANGLES) 9 12 13 39: 25 type=118 (ANGLES) 9 12 14 39: 26 type=120 (ANGLES) 9 12 15 39: 27 type=121 (ANGLES) 13 12 14 39: 28 type=118 (ANGLES) 13 12 15 39: 29 type=118 (ANGLES) 14 12 15 39: 30 type=118 (ANGLES) 12 15 16 39: 31 type=118 (ANGLES) 12 15 17 39: 32 type=117 (ANGLES) 12 15 18 39: 33 type=121 (ANGLES) 16 15 17 39: 34 type=116 (ANGLES) 16 15 18 39: 35 type=116 (ANGLES) 17 15 18 39: 36 type=116 (ANGLES) 15 18 19 39: 37 type=116 (ANGLES) 15 18 20 39: 38 type=116 (ANGLES) 15 18 21 39: 39 type=116 (ANGLES) 19 18 20 39: 40 type=116 (ANGLES) 19 18 21 39: 41 type=116 (ANGLES) 20 18 21 39: 42 type=122 (ANGLES) 4 22 23 39: 43 type=123 (ANGLES) 4 22 24 39: 44 type=124 (ANGLES) 23 22 24 39: 45 type=125 (ANGLES) 22 24 25 39: 46 type=126 (ANGLES) 22 24 26 39: 47 type=127 (ANGLES) 25 24 26 39: 48 type=116 (ANGLES) 24 26 27 39: 49 type=128 (ANGLES) 24 26 28 39: 50 type=129 (ANGLES) 24 26 38 39: 51 type=118 (ANGLES) 27 26 28 39: 52 type=116 (ANGLES) 27 26 38 39: 53 type=119 (ANGLES) 28 26 38 39: 54 type=118 (ANGLES) 26 28 29 39: 55 type=120 (ANGLES) 26 28 30 39: 56 type=120 (ANGLES) 26 28 34 39: 57 type=118 (ANGLES) 29 28 30 39: 58 type=118 (ANGLES) 29 28 34 39: 59 type=120 (ANGLES) 30 28 34 39: 60 type=118 (ANGLES) 28 30 31 39: 61 type=118 (ANGLES) 28 30 32 39: 62 type=118 (ANGLES) 28 30 33 39: 63 type=121 (ANGLES) 31 30 32 39: 64 type=121 (ANGLES) 31 30 33 39: 65 type=121 (ANGLES) 32 30 33 39: 66 type=118 (ANGLES) 28 34 35 39: 67 type=118 (ANGLES) 28 34 36 39: 68 type=118 (ANGLES) 28 34 37 39: 69 type=121 (ANGLES) 35 34 36 39: 70 type=121 (ANGLES) 35 34 37 39: 71 type=121 (ANGLES) 36 34 37 39: 72 type=122 (ANGLES) 26 38 39 39: 73 type=123 (ANGLES) 26 38 40 39: 74 type=124 (ANGLES) 39 38 40 39: 75 type=125 (ANGLES) 38 40 41 39: 76 type=126 (ANGLES) 38 40 42 39: 77 type=127 (ANGLES) 41 40 42 39: 78 type=116 (ANGLES) 40 42 43 39: 79 type=128 (ANGLES) 40 42 44 39: 80 type=129 (ANGLES) 40 42 58 39: 81 type=118 (ANGLES) 43 42 44 39: 82 type=116 (ANGLES) 43 42 58 39: 83 type=119 (ANGLES) 44 42 58 39: 84 type=118 (ANGLES) 42 44 45 39: 85 type=118 (ANGLES) 42 44 46 39: 86 type=130 (ANGLES) 42 44 47 39: 87 type=121 (ANGLES) 45 44 46 39: 88 type=116 (ANGLES) 45 44 47 39: 89 type=116 (ANGLES) 46 44 47 39: 90 type=131 (ANGLES) 44 47 48 39: 91 type=131 (ANGLES) 44 47 50 39: 92 type=132 (ANGLES) 48 47 50 39: 93 type=133 (ANGLES) 47 48 49 39: 94 type=132 (ANGLES) 47 48 52 39: 95 type=133 (ANGLES) 49 48 52 39: 96 type=133 (ANGLES) 47 50 51 39: 97 type=132 (ANGLES) 47 50 54 39: 98 type=133 (ANGLES) 51 50 54 39: 99 type=133 (ANGLES) 48 52 53 39: 100 type=132 (ANGLES) 48 52 56 39: 101 type=133 (ANGLES) 53 52 56 39: 102 type=133 (ANGLES) 50 54 55 39: 103 type=132 (ANGLES) 50 54 56 39: 104 type=133 (ANGLES) 55 54 56 39: 105 type=132 (ANGLES) 52 56 54 39: 106 type=133 (ANGLES) 52 56 57 39: 107 type=133 (ANGLES) 54 56 57 39: 108 type=122 (ANGLES) 42 58 59 39: 109 type=123 (ANGLES) 42 58 60 39: 110 type=124 (ANGLES) 59 58 60 39: 111 type=125 (ANGLES) 58 60 61 39: 112 type=126 (ANGLES) 58 60 62 39: 113 type=127 (ANGLES) 61 60 62 39: 114 type=116 (ANGLES) 60 62 63 39: 115 type=116 (ANGLES) 60 62 64 39: 116 type=129 (ANGLES) 60 62 65 39: 117 type=121 (ANGLES) 63 62 64 39: 118 type=116 (ANGLES) 63 62 65 39: 119 type=116 (ANGLES) 64 62 65 39: 120 type=122 (ANGLES) 62 65 66 39: 121 type=123 (ANGLES) 62 65 67 39: 122 type=124 (ANGLES) 66 65 67 39: 123 type=125 (ANGLES) 65 67 68 39: 124 type=126 (ANGLES) 65 67 69 39: 125 type=127 (ANGLES) 68 67 69 39: 126 type=116 (ANGLES) 67 69 70 39: 127 type=128 (ANGLES) 67 69 71 39: 128 type=129 (ANGLES) 67 69 89 39: 129 type=118 (ANGLES) 70 69 71 39: 130 type=116 (ANGLES) 70 69 89 39: 131 type=119 (ANGLES) 71 69 89 39: 132 type=118 (ANGLES) 69 71 72 39: 133 type=118 (ANGLES) 69 71 73 39: 134 type=120 (ANGLES) 69 71 74 39: 135 type=121 (ANGLES) 72 71 73 39: 136 type=118 (ANGLES) 72 71 74 39: 137 type=118 (ANGLES) 73 71 74 39: 138 type=118 (ANGLES) 71 74 75 39: 139 type=118 (ANGLES) 71 74 76 39: 140 type=120 (ANGLES) 71 74 77 39: 141 type=121 (ANGLES) 75 74 76 39: 142 type=118 (ANGLES) 75 74 77 39: 143 type=118 (ANGLES) 76 74 77 39: 144 type=118 (ANGLES) 74 77 78 39: 145 type=118 (ANGLES) 74 77 79 39: 146 type=117 (ANGLES) 74 77 80 39: 147 type=121 (ANGLES) 78 77 79 39: 148 type=116 (ANGLES) 78 77 80 39: 149 type=116 (ANGLES) 79 77 80 39: 150 type=134 (ANGLES) 77 80 81 39: 151 type=135 (ANGLES) 77 80 82 39: 152 type=133 (ANGLES) 81 80 82 39: 153 type=131 (ANGLES) 80 82 83 39: 154 type=131 (ANGLES) 80 82 86 39: 155 type=131 (ANGLES) 83 82 86 39: 156 type=133 (ANGLES) 82 83 84 39: 157 type=133 (ANGLES) 82 83 85 39: 158 type=133 (ANGLES) 84 83 85 39: 159 type=133 (ANGLES) 82 86 87 39: 160 type=133 (ANGLES) 82 86 88 39: 161 type=133 (ANGLES) 87 86 88 39: 162 type=122 (ANGLES) 69 89 90 39: 163 type=123 (ANGLES) 69 89 91 39: 164 type=124 (ANGLES) 90 89 91 39: 165 type=125 (ANGLES) 89 91 92 39: 166 type=126 (ANGLES) 89 91 93 39: 167 type=127 (ANGLES) 92 91 93 39: 168 type=116 (ANGLES) 91 93 94 39: 169 type=128 (ANGLES) 91 93 95 39: 170 type=129 (ANGLES) 91 93 100 39: 171 type=118 (ANGLES) 94 93 95 39: 172 type=116 (ANGLES) 94 93 100 39: 173 type=119 (ANGLES) 95 93 100 39: 174 type=118 (ANGLES) 93 95 96 39: 175 type=118 (ANGLES) 93 95 97 39: 176 type=136 (ANGLES) 93 95 98 39: 177 type=121 (ANGLES) 96 95 97 39: 178 type=116 (ANGLES) 96 95 98 39: 179 type=116 (ANGLES) 97 95 98 39: 180 type=137 (ANGLES) 95 98 99 39: 181 type=122 (ANGLES) 93 100 101 39: 182 type=123 (ANGLES) 93 100 102 39: 183 type=124 (ANGLES) 101 100 102 39: 184 type=125 (ANGLES) 100 102 103 39: 185 type=126 (ANGLES) 100 102 104 39: 186 type=127 (ANGLES) 103 102 104 39: 187 type=116 (ANGLES) 102 104 105 39: 188 type=128 (ANGLES) 102 104 106 39: 189 type=129 (ANGLES) 102 104 115 39: 190 type=118 (ANGLES) 105 104 106 39: 191 type=116 (ANGLES) 105 104 115 39: 192 type=119 (ANGLES) 106 104 115 39: 193 type=118 (ANGLES) 104 106 107 39: 194 type=118 (ANGLES) 104 106 108 39: 195 type=120 (ANGLES) 104 106 109 39: 196 type=121 (ANGLES) 107 106 108 39: 197 type=118 (ANGLES) 107 106 109 39: 198 type=118 (ANGLES) 108 106 109 39: 199 type=118 (ANGLES) 106 109 110 39: 200 type=118 (ANGLES) 106 109 111 39: 201 type=119 (ANGLES) 106 109 112 39: 202 type=121 (ANGLES) 110 109 111 39: 203 type=116 (ANGLES) 110 109 112 39: 204 type=116 (ANGLES) 111 109 112 39: 205 type=138 (ANGLES) 109 112 113 39: 206 type=138 (ANGLES) 109 112 114 39: 207 type=139 (ANGLES) 113 112 114 39: 208 type=122 (ANGLES) 104 115 116 39: 209 type=123 (ANGLES) 104 115 117 39: 210 type=124 (ANGLES) 116 115 117 39: 211 type=125 (ANGLES) 115 117 118 39: 212 type=126 (ANGLES) 115 117 119 39: 213 type=127 (ANGLES) 118 117 119 39: 214 type=116 (ANGLES) 117 119 120 39: 215 type=128 (ANGLES) 117 119 121 39: 216 type=129 (ANGLES) 117 119 134 39: 217 type=118 (ANGLES) 120 119 121 39: 218 type=116 (ANGLES) 120 119 134 39: 219 type=119 (ANGLES) 121 119 134 39: 220 type=118 (ANGLES) 119 121 122 39: 221 type=118 (ANGLES) 119 121 123 39: 222 type=120 (ANGLES) 119 121 124 39: 223 type=121 (ANGLES) 122 121 123 39: 224 type=118 (ANGLES) 122 121 124 39: 225 type=118 (ANGLES) 123 121 124 39: 226 type=118 (ANGLES) 121 124 125 39: 227 type=120 (ANGLES) 121 124 126 39: 228 type=120 (ANGLES) 121 124 130 39: 229 type=118 (ANGLES) 125 124 126 39: 230 type=118 (ANGLES) 125 124 130 39: 231 type=120 (ANGLES) 126 124 130 39: 232 type=118 (ANGLES) 124 126 127 39: 233 type=118 (ANGLES) 124 126 128 39: 234 type=118 (ANGLES) 124 126 129 39: 235 type=121 (ANGLES) 127 126 128 39: 236 type=121 (ANGLES) 127 126 129 39: 237 type=121 (ANGLES) 128 126 129 39: 238 type=118 (ANGLES) 124 130 131 39: 239 type=118 (ANGLES) 124 130 132 39: 240 type=118 (ANGLES) 124 130 133 39: 241 type=121 (ANGLES) 131 130 132 39: 242 type=121 (ANGLES) 131 130 133 39: 243 type=121 (ANGLES) 132 130 133 39: 244 type=122 (ANGLES) 119 134 135 39: 245 type=123 (ANGLES) 119 134 136 39: 246 type=124 (ANGLES) 135 134 136 39: 247 type=125 (ANGLES) 134 136 137 39: 248 type=126 (ANGLES) 134 136 138 39: 249 type=127 (ANGLES) 137 136 138 39: 250 type=116 (ANGLES) 136 138 139 39: 251 type=128 (ANGLES) 136 138 140 39: 252 type=129 (ANGLES) 136 138 144 39: 253 type=118 (ANGLES) 139 138 140 39: 254 type=116 (ANGLES) 139 138 144 39: 255 type=119 (ANGLES) 140 138 144 39: 256 type=118 (ANGLES) 138 140 141 39: 257 type=118 (ANGLES) 138 140 142 39: 258 type=118 (ANGLES) 138 140 143 39: 259 type=121 (ANGLES) 141 140 142 39: 260 type=121 (ANGLES) 141 140 143 39: 261 type=121 (ANGLES) 142 140 143 39: 262 type=122 (ANGLES) 138 144 145 39: 263 type=123 (ANGLES) 138 144 146 39: 264 type=124 (ANGLES) 145 144 146 39: 265 type=125 (ANGLES) 144 146 147 39: 266 type=126 (ANGLES) 144 146 148 39: 267 type=127 (ANGLES) 147 146 148 39: 268 type=116 (ANGLES) 146 148 149 39: 269 type=128 (ANGLES) 146 148 150 39: 270 type=129 (ANGLES) 146 148 154 39: 271 type=118 (ANGLES) 149 148 150 39: 272 type=116 (ANGLES) 149 148 154 39: 273 type=119 (ANGLES) 150 148 154 39: 274 type=118 (ANGLES) 148 150 151 39: 275 type=118 (ANGLES) 148 150 152 39: 276 type=118 (ANGLES) 148 150 153 39: 277 type=121 (ANGLES) 151 150 152 39: 278 type=121 (ANGLES) 151 150 153 39: 279 type=121 (ANGLES) 152 150 153 39: 280 type=122 (ANGLES) 148 154 155 39: G96Angle: 39: nr: 0 39: Restricted Angles: 39: nr: 0 39: Lin. Angle: 39: nr: 0 39: Bond-Cross: 39: nr: 0 39: BA-Cross: 39: nr: 0 39: U-B: 39: nr: 0 39: Quartic Angles: 39: nr: 0 39: Tab. Angles: 39: nr: 0 39: Proper Dih.: 39: nr: 145 39: iatoms: 39: 0 type=140 (PDIHS) 4 24 22 23 39: 1 type=141 (PDIHS) 22 26 24 25 39: 2 type=140 (PDIHS) 26 40 38 39 39: 3 type=141 (PDIHS) 38 42 40 41 39: 4 type=140 (PDIHS) 42 60 58 59 39: 5 type=142 (PDIHS) 44 47 50 48 39: 6 type=142 (PDIHS) 47 52 48 49 39: 7 type=142 (PDIHS) 47 54 50 51 39: 8 type=142 (PDIHS) 48 56 52 53 39: 9 type=142 (PDIHS) 50 56 54 55 39: 10 type=142 (PDIHS) 52 54 56 57 39: 11 type=141 (PDIHS) 58 62 60 61 39: 12 type=140 (PDIHS) 62 67 65 66 39: 13 type=141 (PDIHS) 65 69 67 68 39: 14 type=140 (PDIHS) 69 91 89 90 39: 15 type=141 (PDIHS) 77 82 80 81 39: 16 type=140 (PDIHS) 80 83 82 86 39: 17 type=141 (PDIHS) 82 84 83 85 39: 18 type=141 (PDIHS) 82 87 86 88 39: 19 type=141 (PDIHS) 89 93 91 92 39: 20 type=140 (PDIHS) 93 102 100 101 39: 21 type=141 (PDIHS) 100 104 102 103 39: 22 type=140 (PDIHS) 104 117 115 116 39: 23 type=140 (PDIHS) 109 113 112 114 39: 24 type=141 (PDIHS) 115 119 117 118 39: 25 type=140 (PDIHS) 119 136 134 135 39: 26 type=141 (PDIHS) 134 138 136 137 39: 27 type=140 (PDIHS) 138 146 144 145 39: 28 type=141 (PDIHS) 144 148 146 147 39: Ryckaert-Bell.: 39: nr: 1565 39: iatoms: 39: 0 type=143 (RBDIHS) 1 0 4 5 39: 1 type=144 (RBDIHS) 1 0 4 6 39: 2 type=144 (RBDIHS) 1 0 4 22 39: 3 type=143 (RBDIHS) 2 0 4 5 39: 4 type=144 (RBDIHS) 2 0 4 6 39: 5 type=144 (RBDIHS) 2 0 4 22 39: 6 type=143 (RBDIHS) 3 0 4 5 39: 7 type=144 (RBDIHS) 3 0 4 6 39: 8 type=144 (RBDIHS) 3 0 4 22 39: 9 type=145 (RBDIHS) 0 4 6 9 39: 10 type=146 (RBDIHS) 22 4 6 9 39: 11 type=147 (RBDIHS) 0 4 6 7 39: 12 type=147 (RBDIHS) 0 4 6 8 39: 13 type=148 (RBDIHS) 5 4 6 7 39: 14 type=148 (RBDIHS) 5 4 6 8 39: 15 type=148 (RBDIHS) 5 4 6 9 39: 16 type=149 (RBDIHS) 22 4 6 7 39: 17 type=149 (RBDIHS) 22 4 6 8 39: 18 type=150 (RBDIHS) 0 4 22 24 39: 19 type=151 (RBDIHS) 6 4 22 24 39: 20 type=148 (RBDIHS) 4 6 9 10 39: 21 type=148 (RBDIHS) 4 6 9 11 39: 22 type=152 (RBDIHS) 4 6 9 12 39: 23 type=148 (RBDIHS) 7 6 9 10 39: 24 type=148 (RBDIHS) 7 6 9 11 39: 25 type=148 (RBDIHS) 7 6 9 12 39: 26 type=148 (RBDIHS) 8 6 9 10 39: 27 type=148 (RBDIHS) 8 6 9 11 39: 28 type=148 (RBDIHS) 8 6 9 12 39: 29 type=148 (RBDIHS) 6 9 12 13 39: 30 type=148 (RBDIHS) 6 9 12 14 39: 31 type=152 (RBDIHS) 6 9 12 15 39: 32 type=148 (RBDIHS) 10 9 12 13 39: 33 type=148 (RBDIHS) 10 9 12 14 39: 34 type=148 (RBDIHS) 10 9 12 15 39: 35 type=148 (RBDIHS) 11 9 12 13 39: 36 type=148 (RBDIHS) 11 9 12 14 39: 37 type=148 (RBDIHS) 11 9 12 15 39: 38 type=148 (RBDIHS) 9 12 15 16 39: 39 type=148 (RBDIHS) 9 12 15 17 39: 40 type=153 (RBDIHS) 9 12 15 18 39: 41 type=148 (RBDIHS) 13 12 15 16 39: 42 type=148 (RBDIHS) 13 12 15 17 39: 43 type=154 (RBDIHS) 13 12 15 18 39: 44 type=148 (RBDIHS) 14 12 15 16 39: 45 type=148 (RBDIHS) 14 12 15 17 39: 46 type=154 (RBDIHS) 14 12 15 18 39: 47 type=144 (RBDIHS) 12 15 18 19 39: 48 type=144 (RBDIHS) 12 15 18 20 39: 49 type=144 (RBDIHS) 12 15 18 21 39: 50 type=143 (RBDIHS) 16 15 18 19 39: 51 type=143 (RBDIHS) 16 15 18 20 39: 52 type=143 (RBDIHS) 16 15 18 21 39: 53 type=143 (RBDIHS) 17 15 18 19 39: 54 type=143 (RBDIHS) 17 15 18 20 39: 55 type=143 (RBDIHS) 17 15 18 21 39: 56 type=155 (RBDIHS) 4 22 24 25 39: 57 type=156 (RBDIHS) 4 22 24 26 39: 58 type=155 (RBDIHS) 23 22 24 25 39: 59 type=157 (RBDIHS) 23 22 24 26 39: 60 type=158 (RBDIHS) 22 24 26 28 39: 61 type=159 (RBDIHS) 22 24 26 38 39: 62 type=160 (RBDIHS) 24 26 28 30 39: 63 type=160 (RBDIHS) 24 26 28 34 39: 64 type=161 (RBDIHS) 38 26 28 30 39: 65 type=161 (RBDIHS) 38 26 28 34 39: 66 type=147 (RBDIHS) 24 26 28 29 39: 67 type=148 (RBDIHS) 27 26 28 29 39: 68 type=148 (RBDIHS) 27 26 28 30 39: 69 type=148 (RBDIHS) 27 26 28 34 39: 70 type=149 (RBDIHS) 38 26 28 29 39: 71 type=150 (RBDIHS) 24 26 38 40 39: 72 type=151 (RBDIHS) 28 26 38 40 39: 73 type=148 (RBDIHS) 26 28 30 31 39: 74 type=148 (RBDIHS) 26 28 30 32 39: 75 type=148 (RBDIHS) 26 28 30 33 39: 76 type=148 (RBDIHS) 29 28 30 31 39: 77 type=148 (RBDIHS) 29 28 30 32 39: 78 type=148 (RBDIHS) 29 28 30 33 39: 79 type=148 (RBDIHS) 34 28 30 31 39: 80 type=148 (RBDIHS) 34 28 30 32 39: 81 type=148 (RBDIHS) 34 28 30 33 39: 82 type=148 (RBDIHS) 26 28 34 35 39: 83 type=148 (RBDIHS) 26 28 34 36 39: 84 type=148 (RBDIHS) 26 28 34 37 39: 85 type=148 (RBDIHS) 29 28 34 35 39: 86 type=148 (RBDIHS) 29 28 34 36 39: 87 type=148 (RBDIHS) 29 28 34 37 39: 88 type=148 (RBDIHS) 30 28 34 35 39: 89 type=148 (RBDIHS) 30 28 34 36 39: 90 type=148 (RBDIHS) 30 28 34 37 39: 91 type=155 (RBDIHS) 26 38 40 41 39: 92 type=156 (RBDIHS) 26 38 40 42 39: 93 type=155 (RBDIHS) 39 38 40 41 39: 94 type=157 (RBDIHS) 39 38 40 42 39: 95 type=158 (RBDIHS) 38 40 42 44 39: 96 type=159 (RBDIHS) 38 40 42 58 39: 97 type=147 (RBDIHS) 40 42 44 45 39: 98 type=147 (RBDIHS) 40 42 44 46 39: 99 type=162 (RBDIHS) 40 42 44 47 39: 100 type=148 (RBDIHS) 43 42 44 45 39: 101 type=148 (RBDIHS) 43 42 44 46 39: 102 type=163 (RBDIHS) 43 42 44 47 39: 103 type=149 (RBDIHS) 58 42 44 45 39: 104 type=149 (RBDIHS) 58 42 44 46 39: 105 type=164 (RBDIHS) 58 42 44 47 39: 106 type=150 (RBDIHS) 40 42 58 60 39: 107 type=151 (RBDIHS) 44 42 58 60 39: 108 type=165 (RBDIHS) 44 47 48 49 39: 109 type=165 (RBDIHS) 44 47 48 52 39: 110 type=165 (RBDIHS) 50 47 48 49 39: 111 type=165 (RBDIHS) 50 47 48 52 39: 112 type=165 (RBDIHS) 44 47 50 51 39: 113 type=165 (RBDIHS) 44 47 50 54 39: 114 type=165 (RBDIHS) 48 47 50 51 39: 115 type=165 (RBDIHS) 48 47 50 54 39: 116 type=165 (RBDIHS) 47 48 52 53 39: 117 type=165 (RBDIHS) 47 48 52 56 39: 118 type=165 (RBDIHS) 49 48 52 53 39: 119 type=165 (RBDIHS) 49 48 52 56 39: 120 type=165 (RBDIHS) 47 50 54 55 39: 121 type=165 (RBDIHS) 47 50 54 56 39: 122 type=165 (RBDIHS) 51 50 54 55 39: 123 type=165 (RBDIHS) 51 50 54 56 39: 124 type=165 (RBDIHS) 48 52 56 54 39: 125 type=165 (RBDIHS) 48 52 56 57 39: 126 type=165 (RBDIHS) 53 52 56 54 39: 127 type=165 (RBDIHS) 53 52 56 57 39: 128 type=165 (RBDIHS) 50 54 56 52 39: 129 type=165 (RBDIHS) 50 54 56 57 39: 130 type=165 (RBDIHS) 55 54 56 52 39: 131 type=165 (RBDIHS) 55 54 56 57 39: 132 type=155 (RBDIHS) 42 58 60 61 39: 133 type=156 (RBDIHS) 42 58 60 62 39: 134 type=155 (RBDIHS) 59 58 60 61 39: 135 type=157 (RBDIHS) 59 58 60 62 39: 136 type=159 (RBDIHS) 58 60 62 65 39: 137 type=150 (RBDIHS) 60 62 65 67 39: 138 type=155 (RBDIHS) 62 65 67 68 39: 139 type=156 (RBDIHS) 62 65 67 69 39: 140 type=155 (RBDIHS) 66 65 67 68 39: 141 type=157 (RBDIHS) 66 65 67 69 39: 142 type=158 (RBDIHS) 65 67 69 71 39: 143 type=159 (RBDIHS) 65 67 69 89 39: 144 type=166 (RBDIHS) 67 69 71 74 39: 145 type=167 (RBDIHS) 89 69 71 74 39: 146 type=147 (RBDIHS) 67 69 71 72 39: 147 type=147 (RBDIHS) 67 69 71 73 39: 148 type=148 (RBDIHS) 70 69 71 72 39: 149 type=148 (RBDIHS) 70 69 71 73 39: 150 type=148 (RBDIHS) 70 69 71 74 39: 151 type=149 (RBDIHS) 89 69 71 72 39: 152 type=149 (RBDIHS) 89 69 71 73 39: 153 type=150 (RBDIHS) 67 69 89 91 39: 154 type=151 (RBDIHS) 71 69 89 91 39: 155 type=148 (RBDIHS) 69 71 74 75 39: 156 type=148 (RBDIHS) 69 71 74 76 39: 157 type=152 (RBDIHS) 69 71 74 77 39: 158 type=148 (RBDIHS) 72 71 74 75 39: 159 type=148 (RBDIHS) 72 71 74 76 39: 160 type=148 (RBDIHS) 72 71 74 77 39: 161 type=148 (RBDIHS) 73 71 74 75 39: 162 type=148 (RBDIHS) 73 71 74 76 39: 163 type=148 (RBDIHS) 73 71 74 77 39: 164 type=148 (RBDIHS) 71 74 77 78 39: 165 type=148 (RBDIHS) 71 74 77 79 39: 166 type=153 (RBDIHS) 71 74 77 80 39: 167 type=148 (RBDIHS) 75 74 77 78 39: 168 type=148 (RBDIHS) 75 74 77 79 39: 169 type=168 (RBDIHS) 75 74 77 80 39: 170 type=148 (RBDIHS) 76 74 77 78 39: 171 type=148 (RBDIHS) 76 74 77 79 39: 172 type=168 (RBDIHS) 76 74 77 80 39: 173 type=169 (RBDIHS) 74 77 80 81 39: 174 type=170 (RBDIHS) 74 77 80 82 39: 175 type=171 (RBDIHS) 78 77 80 82 39: 176 type=171 (RBDIHS) 79 77 80 82 39: 177 type=172 (RBDIHS) 77 80 82 83 39: 178 type=172 (RBDIHS) 77 80 82 86 39: 179 type=173 (RBDIHS) 81 80 82 83 39: 180 type=173 (RBDIHS) 81 80 82 86 39: 181 type=173 (RBDIHS) 80 82 83 84 39: 182 type=173 (RBDIHS) 80 82 83 85 39: 183 type=173 (RBDIHS) 86 82 83 84 39: 184 type=173 (RBDIHS) 86 82 83 85 39: 185 type=173 (RBDIHS) 80 82 86 87 39: 186 type=173 (RBDIHS) 80 82 86 88 39: 187 type=173 (RBDIHS) 83 82 86 87 39: 188 type=173 (RBDIHS) 83 82 86 88 39: 189 type=155 (RBDIHS) 69 89 91 92 39: 190 type=156 (RBDIHS) 69 89 91 93 39: 191 type=155 (RBDIHS) 90 89 91 92 39: 192 type=157 (RBDIHS) 90 89 91 93 39: 193 type=158 (RBDIHS) 89 91 93 95 39: 194 type=159 (RBDIHS) 89 91 93 100 39: 195 type=174 (RBDIHS) 91 93 95 98 39: 196 type=175 (RBDIHS) 100 93 95 98 39: 197 type=147 (RBDIHS) 91 93 95 96 39: 198 type=147 (RBDIHS) 91 93 95 97 39: 199 type=148 (RBDIHS) 94 93 95 96 39: 200 type=148 (RBDIHS) 94 93 95 97 39: 201 type=176 (RBDIHS) 94 93 95 98 39: 202 type=149 (RBDIHS) 100 93 95 96 39: 203 type=149 (RBDIHS) 100 93 95 97 39: 204 type=150 (RBDIHS) 91 93 100 102 39: 205 type=151 (RBDIHS) 95 93 100 102 39: 206 type=177 (RBDIHS) 93 95 98 99 39: 207 type=178 (RBDIHS) 96 95 98 99 39: 208 type=178 (RBDIHS) 97 95 98 99 39: 209 type=155 (RBDIHS) 93 100 102 103 39: 210 type=156 (RBDIHS) 93 100 102 104 39: 211 type=155 (RBDIHS) 101 100 102 103 39: 212 type=157 (RBDIHS) 101 100 102 104 39: 213 type=158 (RBDIHS) 100 102 104 106 39: 214 type=159 (RBDIHS) 100 102 104 115 39: 215 type=179 (RBDIHS) 102 104 106 109 39: 216 type=180 (RBDIHS) 115 104 106 109 39: 217 type=147 (RBDIHS) 102 104 106 107 39: 218 type=147 (RBDIHS) 102 104 106 108 39: 219 type=148 (RBDIHS) 105 104 106 107 39: 220 type=148 (RBDIHS) 105 104 106 108 39: 221 type=148 (RBDIHS) 105 104 106 109 39: 222 type=149 (RBDIHS) 115 104 106 107 39: 223 type=149 (RBDIHS) 115 104 106 108 39: 224 type=150 (RBDIHS) 102 104 115 117 39: 225 type=151 (RBDIHS) 106 104 115 117 39: 226 type=148 (RBDIHS) 104 106 109 110 39: 227 type=148 (RBDIHS) 104 106 109 111 39: 228 type=181 (RBDIHS) 104 106 109 112 39: 229 type=148 (RBDIHS) 107 106 109 110 39: 230 type=148 (RBDIHS) 107 106 109 111 39: 231 type=182 (RBDIHS) 107 106 109 112 39: 232 type=148 (RBDIHS) 108 106 109 110 39: 233 type=148 (RBDIHS) 108 106 109 111 39: 234 type=182 (RBDIHS) 108 106 109 112 39: 235 type=183 (RBDIHS) 106 109 112 113 39: 236 type=183 (RBDIHS) 106 109 112 114 39: 237 type=155 (RBDIHS) 104 115 117 118 39: 238 type=156 (RBDIHS) 104 115 117 119 39: 239 type=155 (RBDIHS) 116 115 117 118 39: 240 type=157 (RBDIHS) 116 115 117 119 39: 241 type=158 (RBDIHS) 115 117 119 121 39: 242 type=159 (RBDIHS) 115 117 119 134 39: 243 type=184 (RBDIHS) 117 119 121 124 39: 244 type=185 (RBDIHS) 134 119 121 124 39: 245 type=147 (RBDIHS) 117 119 121 122 39: 246 type=147 (RBDIHS) 117 119 121 123 39: 247 type=148 (RBDIHS) 120 119 121 122 39: 248 type=148 (RBDIHS) 120 119 121 123 39: 249 type=148 (RBDIHS) 120 119 121 124 39: 250 type=149 (RBDIHS) 134 119 121 122 39: 251 type=149 (RBDIHS) 134 119 121 123 39: 252 type=150 (RBDIHS) 117 119 134 136 39: 253 type=151 (RBDIHS) 121 119 134 136 39: 254 type=148 (RBDIHS) 119 121 124 125 39: 255 type=152 (RBDIHS) 119 121 124 126 39: 256 type=152 (RBDIHS) 119 121 124 130 39: 257 type=148 (RBDIHS) 122 121 124 125 39: 258 type=148 (RBDIHS) 122 121 124 126 39: 259 type=148 (RBDIHS) 122 121 124 130 39: 260 type=148 (RBDIHS) 123 121 124 125 39: 261 type=148 (RBDIHS) 123 121 124 126 39: 262 type=148 (RBDIHS) 123 121 124 130 39: 263 type=148 (RBDIHS) 121 124 126 127 39: 264 type=148 (RBDIHS) 121 124 126 128 39: 265 type=148 (RBDIHS) 121 124 126 129 39: 266 type=148 (RBDIHS) 125 124 126 127 39: 267 type=148 (RBDIHS) 125 124 126 128 39: 268 type=148 (RBDIHS) 125 124 126 129 39: 269 type=148 (RBDIHS) 130 124 126 127 39: 270 type=148 (RBDIHS) 130 124 126 128 39: 271 type=148 (RBDIHS) 130 124 126 129 39: 272 type=148 (RBDIHS) 121 124 130 131 39: 273 type=148 (RBDIHS) 121 124 130 132 39: 274 type=148 (RBDIHS) 121 124 130 133 39: 275 type=148 (RBDIHS) 125 124 130 131 39: 276 type=148 (RBDIHS) 125 124 130 132 39: 277 type=148 (RBDIHS) 125 124 130 133 39: 278 type=148 (RBDIHS) 126 124 130 131 39: 279 type=148 (RBDIHS) 126 124 130 132 39: 280 type=148 (RBDIHS) 126 124 130 133 39: 281 type=155 (RBDIHS) 119 134 136 137 39: 282 type=156 (RBDIHS) 119 134 136 138 39: 283 type=155 (RBDIHS) 135 134 136 137 39: 284 type=157 (RBDIHS) 135 134 136 138 39: 285 type=158 (RBDIHS) 134 136 138 140 39: 286 type=159 (RBDIHS) 134 136 138 144 39: 287 type=147 (RBDIHS) 136 138 140 141 39: 288 type=147 (RBDIHS) 136 138 140 142 39: 289 type=147 (RBDIHS) 136 138 140 143 39: 290 type=148 (RBDIHS) 139 138 140 141 39: 291 type=148 (RBDIHS) 139 138 140 142 39: 292 type=148 (RBDIHS) 139 138 140 143 39: 293 type=149 (RBDIHS) 144 138 140 141 39: 294 type=149 (RBDIHS) 144 138 140 142 39: 295 type=149 (RBDIHS) 144 138 140 143 39: 296 type=150 (RBDIHS) 136 138 144 146 39: 297 type=151 (RBDIHS) 140 138 144 146 39: 298 type=155 (RBDIHS) 138 144 146 147 39: 299 type=156 (RBDIHS) 138 144 146 148 39: 300 type=155 (RBDIHS) 145 144 146 147 39: 301 type=157 (RBDIHS) 145 144 146 148 39: 302 type=158 (RBDIHS) 144 146 148 150 39: 303 type=159 (RBDIHS) 144 146 148 154 39: 304 type=147 (RBDIHS) 146 148 150 151 39: 305 type=147 (RBDIHS) 146 148 150 152 39: 306 type=147 (RBDIHS) 146 148 150 153 39: 307 type=148 (RBDIHS) 149 148 150 151 39: 308 type=148 (RBDIHS) 149 148 150 152 39: 309 type=148 (RBDIHS) 149 148 150 153 39: 310 type=149 (RBDIHS) 154 148 150 151 39: 311 type=149 (RBDIHS) 154 148 150 152 39: 312 type=149 (RBDIHS) 154 148 150 153 39: Restricted Dih.: 39: nr: 0 39: CBT Dih.: 39: nr: 0 39: Fourier Dih.: 39: nr: 0 39: Improper Dih.: 39: nr: 0 39: Improper Dih.: 39: nr: 0 39: Tab. Dih.: 39: nr: 0 39: CMAP Dih.: 39: nr: 0 39: GB 1-2 Pol. (unused): 39: nr: 0 39: GB 1-3 Pol. (unused): 39: nr: 0 39: GB 1-4 Pol. (unused): 39: nr: 0 39: GB Polarization (unused): 39: nr: 0 39: Nonpolar Sol. (unused): 39: nr: 0 39: LJ-14: 39: nr: 1197 39: iatoms: 39: 0 type=186 (LJ14) 0 7 39: 1 type=186 (LJ14) 0 8 39: 2 type=187 (LJ14) 0 9 39: 3 type=188 (LJ14) 0 23 39: 4 type=189 (LJ14) 0 24 39: 5 type=190 (LJ14) 1 5 39: 6 type=190 (LJ14) 1 6 39: 7 type=190 (LJ14) 1 22 39: 8 type=190 (LJ14) 2 5 39: 9 type=190 (LJ14) 2 6 39: 10 type=190 (LJ14) 2 22 39: 11 type=190 (LJ14) 3 5 39: 12 type=190 (LJ14) 3 6 39: 13 type=190 (LJ14) 3 22 39: 14 type=191 (LJ14) 4 10 39: 15 type=191 (LJ14) 4 11 39: 16 type=192 (LJ14) 4 12 39: 17 type=190 (LJ14) 4 25 39: 18 type=192 (LJ14) 4 26 39: 19 type=193 (LJ14) 5 7 39: 20 type=193 (LJ14) 5 8 39: 21 type=191 (LJ14) 5 9 39: 22 type=194 (LJ14) 5 23 39: 23 type=186 (LJ14) 5 24 39: 24 type=191 (LJ14) 6 13 39: 25 type=191 (LJ14) 6 14 39: 26 type=192 (LJ14) 6 15 39: 27 type=195 (LJ14) 6 23 39: 28 type=187 (LJ14) 6 24 39: 29 type=193 (LJ14) 7 10 39: 30 type=193 (LJ14) 7 11 39: 31 type=191 (LJ14) 7 12 39: 32 type=196 (LJ14) 7 22 39: 33 type=193 (LJ14) 8 10 39: 34 type=193 (LJ14) 8 11 39: 35 type=191 (LJ14) 8 12 39: 36 type=196 (LJ14) 8 22 39: 37 type=191 (LJ14) 9 16 39: 38 type=191 (LJ14) 9 17 39: 39 type=187 (LJ14) 9 18 39: 40 type=197 (LJ14) 9 22 39: 41 type=193 (LJ14) 10 13 39: 42 type=193 (LJ14) 10 14 39: 43 type=191 (LJ14) 10 15 39: 44 type=193 (LJ14) 11 13 39: 45 type=193 (LJ14) 11 14 39: 46 type=191 (LJ14) 11 15 39: 47 type=190 (LJ14) 12 19 39: 48 type=190 (LJ14) 12 20 39: 49 type=190 (LJ14) 12 21 39: 50 type=193 (LJ14) 13 16 39: 51 type=193 (LJ14) 13 17 39: 52 type=186 (LJ14) 13 18 39: 53 type=193 (LJ14) 14 16 39: 54 type=193 (LJ14) 14 17 39: 55 type=186 (LJ14) 14 18 39: 56 type=190 (LJ14) 16 19 39: 57 type=190 (LJ14) 16 20 39: 58 type=190 (LJ14) 16 21 39: 59 type=190 (LJ14) 17 19 39: 60 type=190 (LJ14) 17 20 39: 61 type=190 (LJ14) 17 21 39: 62 type=196 (LJ14) 22 27 39: 63 type=197 (LJ14) 22 28 39: 64 type=198 (LJ14) 22 38 39: 65 type=190 (LJ14) 23 25 39: 66 type=195 (LJ14) 23 26 39: 67 type=186 (LJ14) 24 29 39: 68 type=187 (LJ14) 24 30 39: 69 type=187 (LJ14) 24 34 39: 70 type=188 (LJ14) 24 39 39: 71 type=189 (LJ14) 24 40 39: 72 type=190 (LJ14) 25 27 39: 73 type=190 (LJ14) 25 28 39: 74 type=190 (LJ14) 25 38 39: 75 type=191 (LJ14) 26 31 39: 76 type=191 (LJ14) 26 32 39: 77 type=191 (LJ14) 26 33 39: 78 type=191 (LJ14) 26 35 39: 79 type=191 (LJ14) 26 36 39: 80 type=191 (LJ14) 26 37 39: 81 type=190 (LJ14) 26 41 39: 82 type=192 (LJ14) 26 42 39: 83 type=193 (LJ14) 27 29 39: 84 type=191 (LJ14) 27 30 39: 85 type=191 (LJ14) 27 34 39: 86 type=194 (LJ14) 27 39 39: 87 type=186 (LJ14) 27 40 39: 88 type=195 (LJ14) 28 39 39: 89 type=187 (LJ14) 28 40 39: 90 type=193 (LJ14) 29 31 39: 91 type=193 (LJ14) 29 32 39: 92 type=193 (LJ14) 29 33 39: 93 type=193 (LJ14) 29 35 39: 94 type=193 (LJ14) 29 36 39: 95 type=193 (LJ14) 29 37 39: 96 type=196 (LJ14) 29 38 39: 97 type=191 (LJ14) 30 35 39: 98 type=191 (LJ14) 30 36 39: 99 type=191 (LJ14) 30 37 39: 100 type=197 (LJ14) 30 38 39: 101 type=191 (LJ14) 31 34 39: 102 type=191 (LJ14) 32 34 39: 103 type=191 (LJ14) 33 34 39: 104 type=197 (LJ14) 34 38 39: 105 type=196 (LJ14) 38 43 39: 106 type=197 (LJ14) 38 44 39: 107 type=198 (LJ14) 38 58 39: 108 type=190 (LJ14) 39 41 39: 109 type=195 (LJ14) 39 42 39: 110 type=186 (LJ14) 40 45 39: 111 type=186 (LJ14) 40 46 39: 112 type=199 (LJ14) 40 47 39: 113 type=188 (LJ14) 40 59 39: 114 type=189 (LJ14) 40 60 39: 115 type=190 (LJ14) 41 43 39: 116 type=190 (LJ14) 41 44 39: 117 type=190 (LJ14) 41 58 39: 118 type=200 (LJ14) 42 48 39: 119 type=200 (LJ14) 42 50 39: 120 type=190 (LJ14) 42 61 39: 121 type=192 (LJ14) 42 62 39: 122 type=193 (LJ14) 43 45 39: 123 type=193 (LJ14) 43 46 39: 124 type=201 (LJ14) 43 47 39: 125 type=194 (LJ14) 43 59 39: 126 type=186 (LJ14) 43 60 39: 127 type=202 (LJ14) 44 49 39: 128 type=202 (LJ14) 44 51 39: 129 type=200 (LJ14) 44 52 39: 130 type=200 (LJ14) 44 54 39: 131 type=195 (LJ14) 44 59 39: 132 type=187 (LJ14) 44 60 39: 133 type=201 (LJ14) 45 48 39: 134 type=201 (LJ14) 45 50 39: 135 type=196 (LJ14) 45 58 39: 136 type=201 (LJ14) 46 48 39: 137 type=201 (LJ14) 46 50 39: 138 type=196 (LJ14) 46 58 39: 139 type=203 (LJ14) 47 53 39: 140 type=203 (LJ14) 47 55 39: 141 type=204 (LJ14) 47 56 39: 142 type=205 (LJ14) 47 58 39: 143 type=203 (LJ14) 48 51 39: 144 type=204 (LJ14) 48 54 39: 145 type=203 (LJ14) 48 57 39: 146 type=203 (LJ14) 49 50 39: 147 type=206 (LJ14) 49 53 39: 148 type=203 (LJ14) 49 56 39: 149 type=204 (LJ14) 50 52 39: 150 type=203 (LJ14) 50 57 39: 151 type=206 (LJ14) 51 55 39: 152 type=203 (LJ14) 51 56 39: 153 type=203 (LJ14) 52 55 39: 154 type=203 (LJ14) 53 54 39: 155 type=206 (LJ14) 53 57 39: 156 type=206 (LJ14) 55 57 39: 157 type=196 (LJ14) 58 63 39: 158 type=196 (LJ14) 58 64 39: 159 type=198 (LJ14) 58 65 39: 160 type=190 (LJ14) 59 61 39: 161 type=195 (LJ14) 59 62 39: 162 type=188 (LJ14) 60 66 39: 163 type=189 (LJ14) 60 67 39: 164 type=190 (LJ14) 61 63 39: 165 type=190 (LJ14) 61 64 39: 166 type=190 (LJ14) 61 65 39: 167 type=190 (LJ14) 62 68 39: 168 type=192 (LJ14) 62 69 39: 169 type=194 (LJ14) 63 66 39: 170 type=186 (LJ14) 63 67 39: 171 type=194 (LJ14) 64 66 39: 172 type=186 (LJ14) 64 67 39: 173 type=196 (LJ14) 65 70 39: 174 type=197 (LJ14) 65 71 39: 175 type=198 (LJ14) 65 89 39: 176 type=190 (LJ14) 66 68 39: 177 type=195 (LJ14) 66 69 39: 178 type=186 (LJ14) 67 72 39: 179 type=186 (LJ14) 67 73 39: 180 type=187 (LJ14) 67 74 39: 181 type=188 (LJ14) 67 90 39: 182 type=189 (LJ14) 67 91 39: 183 type=190 (LJ14) 68 70 39: 184 type=190 (LJ14) 68 71 39: 185 type=190 (LJ14) 68 89 39: 186 type=191 (LJ14) 69 75 39: 187 type=191 (LJ14) 69 76 39: 188 type=192 (LJ14) 69 77 39: 189 type=190 (LJ14) 69 92 39: 190 type=192 (LJ14) 69 93 39: 191 type=193 (LJ14) 70 72 39: 192 type=193 (LJ14) 70 73 39: 193 type=191 (LJ14) 70 74 39: 194 type=194 (LJ14) 70 90 39: 195 type=186 (LJ14) 70 91 39: 196 type=191 (LJ14) 71 78 39: 197 type=191 (LJ14) 71 79 39: 198 type=187 (LJ14) 71 80 39: 199 type=195 (LJ14) 71 90 39: 200 type=187 (LJ14) 71 91 39: 201 type=193 (LJ14) 72 75 39: 202 type=193 (LJ14) 72 76 39: 203 type=191 (LJ14) 72 77 39: 204 type=196 (LJ14) 72 89 39: 205 type=193 (LJ14) 73 75 39: 206 type=193 (LJ14) 73 76 39: 207 type=191 (LJ14) 73 77 39: 208 type=196 (LJ14) 73 89 39: 209 type=190 (LJ14) 74 81 39: 210 type=207 (LJ14) 74 82 39: 211 type=197 (LJ14) 74 89 39: 212 type=193 (LJ14) 75 78 39: 213 type=193 (LJ14) 75 79 39: 214 type=186 (LJ14) 75 80 39: 215 type=193 (LJ14) 76 78 39: 216 type=193 (LJ14) 76 79 39: 217 type=186 (LJ14) 76 80 39: 218 type=187 (LJ14) 77 83 39: 219 type=187 (LJ14) 77 86 39: 220 type=190 (LJ14) 78 81 39: 221 type=208 (LJ14) 78 82 39: 222 type=190 (LJ14) 79 81 39: 223 type=208 (LJ14) 79 82 39: 224 type=190 (LJ14) 80 84 39: 225 type=190 (LJ14) 80 85 39: 226 type=190 (LJ14) 80 87 39: 227 type=190 (LJ14) 80 88 39: 228 type=190 (LJ14) 81 83 39: 229 type=190 (LJ14) 81 86 39: 230 type=190 (LJ14) 83 87 39: 231 type=190 (LJ14) 83 88 39: 232 type=190 (LJ14) 84 86 39: 233 type=190 (LJ14) 85 86 39: 234 type=196 (LJ14) 89 94 39: 235 type=197 (LJ14) 89 95 39: 236 type=198 (LJ14) 89 100 39: 237 type=190 (LJ14) 90 92 39: 238 type=195 (LJ14) 90 93 39: 239 type=186 (LJ14) 91 96 39: 240 type=186 (LJ14) 91 97 39: 241 type=209 (LJ14) 91 98 39: 242 type=188 (LJ14) 91 101 39: 243 type=189 (LJ14) 91 102 39: 244 type=190 (LJ14) 92 94 39: 245 type=190 (LJ14) 92 95 39: 246 type=190 (LJ14) 92 100 39: 247 type=190 (LJ14) 93 99 39: 248 type=190 (LJ14) 93 103 39: 249 type=192 (LJ14) 93 104 39: 250 type=193 (LJ14) 94 96 39: 251 type=193 (LJ14) 94 97 39: 252 type=210 (LJ14) 94 98 39: 253 type=194 (LJ14) 94 101 39: 254 type=186 (LJ14) 94 102 39: 255 type=195 (LJ14) 95 101 39: 256 type=187 (LJ14) 95 102 39: 257 type=190 (LJ14) 96 99 39: 258 type=196 (LJ14) 96 100 39: 259 type=190 (LJ14) 97 99 39: 260 type=196 (LJ14) 97 100 39: 261 type=211 (LJ14) 98 100 39: 262 type=196 (LJ14) 100 105 39: 263 type=197 (LJ14) 100 106 39: 264 type=198 (LJ14) 100 115 39: 265 type=190 (LJ14) 101 103 39: 266 type=195 (LJ14) 101 104 39: 267 type=186 (LJ14) 102 107 39: 268 type=186 (LJ14) 102 108 39: 269 type=187 (LJ14) 102 109 39: 270 type=188 (LJ14) 102 116 39: 271 type=189 (LJ14) 102 117 39: 272 type=190 (LJ14) 103 105 39: 273 type=190 (LJ14) 103 106 39: 274 type=190 (LJ14) 103 115 39: 275 type=191 (LJ14) 104 110 39: 276 type=191 (LJ14) 104 111 39: 277 type=197 (LJ14) 104 112 39: 278 type=190 (LJ14) 104 118 39: 279 type=192 (LJ14) 104 119 39: 280 type=193 (LJ14) 105 107 39: 281 type=193 (LJ14) 105 108 39: 282 type=191 (LJ14) 105 109 39: 283 type=194 (LJ14) 105 116 39: 284 type=186 (LJ14) 105 117 39: 285 type=195 (LJ14) 106 113 39: 286 type=195 (LJ14) 106 114 39: 287 type=195 (LJ14) 106 116 39: 288 type=187 (LJ14) 106 117 39: 289 type=193 (LJ14) 107 110 39: 290 type=193 (LJ14) 107 111 39: 291 type=196 (LJ14) 107 112 39: 292 type=196 (LJ14) 107 115 39: 293 type=193 (LJ14) 108 110 39: 294 type=193 (LJ14) 108 111 39: 295 type=196 (LJ14) 108 112 39: 296 type=196 (LJ14) 108 115 39: 297 type=197 (LJ14) 109 115 39: 298 type=194 (LJ14) 110 113 39: 299 type=194 (LJ14) 110 114 39: 300 type=194 (LJ14) 111 113 39: 301 type=194 (LJ14) 111 114 39: 302 type=196 (LJ14) 115 120 39: 303 type=197 (LJ14) 115 121 39: 304 type=198 (LJ14) 115 134 39: 305 type=190 (LJ14) 116 118 39: 306 type=195 (LJ14) 116 119 39: 307 type=186 (LJ14) 117 122 39: 308 type=186 (LJ14) 117 123 39: 309 type=187 (LJ14) 117 124 39: 310 type=188 (LJ14) 117 135 39: 311 type=189 (LJ14) 117 136 39: 312 type=190 (LJ14) 118 120 39: 313 type=190 (LJ14) 118 121 39: 314 type=190 (LJ14) 118 134 39: 315 type=191 (LJ14) 119 125 39: 316 type=192 (LJ14) 119 126 39: 317 type=192 (LJ14) 119 130 39: 318 type=190 (LJ14) 119 137 39: 319 type=192 (LJ14) 119 138 39: 320 type=193 (LJ14) 120 122 39: 321 type=193 (LJ14) 120 123 39: 322 type=191 (LJ14) 120 124 39: 323 type=194 (LJ14) 120 135 39: 324 type=186 (LJ14) 120 136 39: 325 type=191 (LJ14) 121 127 39: 326 type=191 (LJ14) 121 128 39: 327 type=191 (LJ14) 121 129 39: 328 type=191 (LJ14) 121 131 39: 329 type=191 (LJ14) 121 132 39: 330 type=191 (LJ14) 121 133 39: 331 type=195 (LJ14) 121 135 39: 332 type=187 (LJ14) 121 136 39: 333 type=193 (LJ14) 122 125 39: 334 type=191 (LJ14) 122 126 39: 335 type=191 (LJ14) 122 130 39: 336 type=196 (LJ14) 122 134 39: 337 type=193 (LJ14) 123 125 39: 338 type=191 (LJ14) 123 126 39: 339 type=191 (LJ14) 123 130 39: 340 type=196 (LJ14) 123 134 39: 341 type=197 (LJ14) 124 134 39: 342 type=193 (LJ14) 125 127 39: 343 type=193 (LJ14) 125 128 39: 344 type=193 (LJ14) 125 129 39: 345 type=193 (LJ14) 125 131 39: 346 type=193 (LJ14) 125 132 39: 347 type=193 (LJ14) 125 133 39: 348 type=191 (LJ14) 126 131 39: 349 type=191 (LJ14) 126 132 39: 350 type=191 (LJ14) 126 133 39: 351 type=191 (LJ14) 127 130 39: 352 type=191 (LJ14) 128 130 39: 353 type=191 (LJ14) 129 130 39: 354 type=196 (LJ14) 134 139 39: 355 type=197 (LJ14) 134 140 39: 356 type=198 (LJ14) 134 144 39: 357 type=190 (LJ14) 135 137 39: 358 type=195 (LJ14) 135 138 39: 359 type=186 (LJ14) 136 141 39: 360 type=186 (LJ14) 136 142 39: 361 type=186 (LJ14) 136 143 39: 362 type=188 (LJ14) 136 145 39: 363 type=189 (LJ14) 136 146 39: 364 type=190 (LJ14) 137 139 39: 365 type=190 (LJ14) 137 140 39: 366 type=190 (LJ14) 137 144 39: 367 type=190 (LJ14) 138 147 39: 368 type=192 (LJ14) 138 148 39: 369 type=193 (LJ14) 139 141 39: 370 type=193 (LJ14) 139 142 39: 371 type=193 (LJ14) 139 143 39: 372 type=194 (LJ14) 139 145 39: 373 type=186 (LJ14) 139 146 39: 374 type=195 (LJ14) 140 145 39: 375 type=187 (LJ14) 140 146 39: 376 type=196 (LJ14) 141 144 39: 377 type=196 (LJ14) 142 144 39: 378 type=196 (LJ14) 143 144 39: 379 type=196 (LJ14) 144 149 39: 380 type=197 (LJ14) 144 150 39: 381 type=198 (LJ14) 144 154 39: 382 type=190 (LJ14) 145 147 39: 383 type=195 (LJ14) 145 148 39: 384 type=186 (LJ14) 146 151 39: 385 type=186 (LJ14) 146 152 39: 386 type=186 (LJ14) 146 153 39: 387 type=188 (LJ14) 146 155 39: 388 type=190 (LJ14) 147 149 39: 389 type=190 (LJ14) 147 150 39: 390 type=190 (LJ14) 147 154 39: 391 type=193 (LJ14) 149 151 39: 392 type=193 (LJ14) 149 152 39: 393 type=193 (LJ14) 149 153 39: 394 type=194 (LJ14) 149 155 39: 395 type=195 (LJ14) 150 155 39: 396 type=196 (LJ14) 151 154 39: 397 type=196 (LJ14) 152 154 39: 398 type=196 (LJ14) 153 154 39: Coulomb-14: 39: nr: 0 39: LJC-14 q: 39: nr: 0 39: LJC Pairs NB: 39: nr: 0 39: LJ (SR): 39: nr: 0 39: Buck.ham (SR): 39: nr: 0 39: LJ (unused): 39: nr: 0 39: B.ham (unused): 39: nr: 0 39: Disper. corr.: 39: nr: 0 39: Coulomb (SR): 39: nr: 0 39: Coul (unused): 39: nr: 0 39: RF excl.: 39: nr: 0 39: Coul. recip.: 39: nr: 0 39: LJ recip.: 39: nr: 0 39: DPD: 39: nr: 0 39: Polarization: 39: nr: 0 39: Water Pol.: 39: nr: 0 39: Thole Pol.: 39: nr: 0 39: Anharm. Pol.: 39: nr: 0 39: Position Rest.: 39: nr: 0 39: Flat-bottom posres: 39: nr: 0 39: Dis. Rest.: 39: nr: 0 39: D.R.Viol. (nm): 39: nr: 0 39: Orient. Rest.: 39: nr: 0 39: Ori. R. RMSD: 39: nr: 0 39: Angle Rest.: 39: nr: 0 39: Angle Rest. Z: 39: nr: 0 39: Dih. Rest.: 39: nr: 0 39: Dih. Rest. Viol.: 39: nr: 0 39: Constraint: 39: nr: 0 39: Constr. No Conn.: 39: nr: 0 39: Settle: 39: nr: 0 39: Virtual site 2: 39: nr: 0 39: Virtual site 2fd: 39: nr: 0 39: Virtual site 3: 39: nr: 0 39: Virtual site 3fd: 39: nr: 0 39: Virtual site 3fad: 39: nr: 0 39: Virtual site 3out: 39: nr: 0 39: Virtual site 4fd: 39: nr: 0 39: Virtual site 4fdn: 39: nr: 0 39: Virtual site N: 39: nr: 0 39: COM Pull En.: 39: nr: 0 39: Density fitting: 39: nr: 0 39: Quantum En.: 39: nr: 0 39: Potential: 39: nr: 0 39: Kinetic En.: 39: nr: 0 39: Total Energy: 39: nr: 0 39: Conserved En.: 39: nr: 0 39: Temperature: 39: nr: 0 39: Vir. Temp. (not used): 39: nr: 0 39: Pres. DC: 39: nr: 0 39: Pressure: 39: nr: 0 39: dH/dl constr.: 39: nr: 0 39: dVremain/dl: 39: nr: 0 39: dEkin/dl: 39: nr: 0 39: dVcoul/dl: 39: nr: 0 39: dVvdw/dl: 39: nr: 0 39: dVbonded/dl: 39: nr: 0 39: dVrestraint/dl: 39: nr: 0 39: dVtemperature/dl: 39: nr: 0 39: grp[T-Coupling ] nr=1, name=[ rest] 39: grp[Energy Mon. ] nr=1, name=[ rest] 39: grp[Acceleration] nr=1, name=[ rest] 39: grp[Freeze ] nr=1, name=[ rest] 39: grp[User1 ] nr=1, name=[ rest] 39: grp[User2 ] nr=1, name=[ rest] 39: grp[VCM ] nr=1, name=[ rest] 39: grp[Compressed X] nr=1, name=[ rest] 39: grp[Or. Res. Fit] nr=1, name=[ rest] 39: grp[QMMM ] nr=1, name=[ rest] 39: grpname (11): 39: grpname[0]={name="System"} 39: grpname[1]={name="Protein"} 39: grpname[2]={name="Protein-H"} 39: grpname[3]={name="C-alpha"} 39: grpname[4]={name="Backbone"} 39: grpname[5]={name="MainChain"} 39: grpname[6]={name="MainChain+Cb"} 39: grpname[7]={name="MainChain+H"} 39: grpname[8]={name="SideChain"} 39: grpname[9]={name="SideChain-H"} 39: grpname[10]={name="rest"} 39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM 39: allocated 0 0 0 0 0 0 0 0 0 0 39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 39: box (3x3): 39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 39: box_rel (3x3): 39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv (3x3): 39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev (3x3): 39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev (3x3): 39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev (3x3): 39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: nosehoover_xi: not available 39: x (156x3): 39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 39: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 39: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 39: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 39: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 39: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 39: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 39: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 39: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 39: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 39: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 39: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 39: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 39: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 39: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 39: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 39: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 39: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 39: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 39: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 39: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 39: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 39: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 39: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 39: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 39: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 39: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 39: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 39: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 39: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 39: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 39: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 39: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 39: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 39: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 39: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 39: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 39: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 39: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 39: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 39: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 39: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 39: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 39: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 39: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 39: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 39: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 39: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 39: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 39: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 39: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 39: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 39: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 39: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 39: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 39: x[ 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0.00000e+00} 39: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: Group statistics 39: T-Coupling : 156 (total 156 atoms) 39: Energy Mon. : 156 (total 156 atoms) 39: Acceleration: 156 (total 156 atoms) 39: Freeze : 156 (total 156 atoms) 39: User1 : 156 (total 156 atoms) 39: User2 : 156 (total 156 atoms) 39: VCM : 156 (total 156 atoms) 39: Compressed X: 156 (total 156 atoms) 39: Or. Res. Fit: 156 (total 156 atoms) 39: QMMM : 156 (total 156 atoms) 39: [ OK ] DumpTest.WorksWithTpr (27 ms) 39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (1 ms) 39: [----------] 2 tests from DumpTest (28 ms total) 39: 39: [----------] 4 tests from ReportMethodsTest 39: 39: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: For a correct single-point energy evaluation with nsteps = 0, use 39: continuation = yes to avoid constraining the input coordinates. 39: 39: Setting the LD random seed to -134240267 39: Generated 330891 of the 330891 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 330891 of the 330891 1-4 parameter combinations 39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 39: 39: NOTE 2 [file lysozyme.top, line 1465]: 39: System has non-zero total charge: 2.000000 39: Total charge should normally be an integer. See 39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 39: for discussion on how close it should be to an integer. 39: 39: 39: 39: Number of degrees of freedom in T-Coupling group rest is 465.00 39: 39: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: NVE simulation with an initial temperature of zero: will use a Verlet 39: buffer of 10%. Check your energy drift! 39: 39: 39: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: You are using a plain Coulomb cut-off, which might produce artifacts. 39: You might want to consider using PME electrostatics. 39: 39: 39: 39: There were 4 notes 39: Analysing residue names: 39: There are: 10 Protein residues 39: Analysing Protein... 39: This run will generate roughly 0 Mb of data 39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 39: [ RUN ] ReportMethodsTest.WritesCorrectInformation 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms) 39: [ RUN ] ReportMethodsTest.ToolEndToEndTest 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: section: Methods 39: subsection: Simulation system 39: A system of 1 molecules (156 atoms) was simulated. 39: 39: subsection: Simulation settings 39: A total of 0 ns were simulated with a time step of 1 fs. 39: Neighbor searching was performed every 10 steps. 39: The Cut-off algorithm was used for electrostatic interactions. 39: with a cut-off of 1 nm. 39: A single cut-off of 1.1 nm was used for Van der Waals interactions. 39: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 39: [----------] 4 tests from ReportMethodsTest (1 ms total) 39: 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: trr version: GMX_trn_file (single precision) 39: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (4 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (2 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from gro file '', 6 atoms. 39: Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (2 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 39: -> frame 0 time 0.000 't= 0.00000', 6 atoms 39: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (2 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (1 ms) 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (12 ms total) 39: 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (0 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from gro file '', 6 atoms. 39: Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (0 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 39: -> frame 0 time 0.000 't= 0.00000', 6 atoms 39: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (0 ms) 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (3 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 18 tests from 4 test cases ran. (1226 ms total) 39: [ PASSED ] 18 tests. 39/54 Test #39: ToolUnitTests ....................... Passed 1.26 sec test 40 Start 40: FileIOTests 40: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/FileIOTests.xml" 40: Test timeout computed to be: 30 40: [==========] Running 33 tests from 8 test cases. 40: [----------] Global test environment set-up. 40: [----------] 2 tests from FileMD5Test 40: [ RUN ] FileMD5Test.CanComputeMD5 40: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 40: [----------] 2 tests from FileMD5Test (1 ms total) 40: 40: [----------] 3 tests from MrcSerializer 40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (1 ms) 40: [----------] 3 tests from MrcSerializer (1 ms total) 40: 40: [----------] 4 tests from MrcDensityMap 40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (1 ms) 40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms) 40: [----------] 4 tests from MrcDensityMap (3 ms total) 40: 40: [----------] 8 tests from MrcDensityMapHeaderTest 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.IsSane 40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 40: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 40: 40: [----------] 9 tests from ReadTest 40: [ RUN ] ReadTest.get_eint_ReadsInteger 40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side '0.8' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 40: [ RUN ] ReadTest.get_eint_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 40: [ RUN ] ReadTest.get_eint64_ReadsInteger 40: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side '0.8' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 40: [ RUN ] ReadTest.get_eint64_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 40: [ RUN ] ReadTest.get_ereal_ReadsInteger 40: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_ereal_ReadsFloat 40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 40: [ RUN ] ReadTest.get_ereal_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not a 40: real value 40: 40: 40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 40: [----------] 9 tests from ReadTest (1 ms total) 40: 40: [----------] 1 test from FileIOXdrSerializerTest 40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 40: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 40: 40: [----------] 2 tests from TngTest 40: [ RUN ] TngTest.CanOpenTngFile 40: TNG library: Cannot open file spc2-traj.tng. /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c: 890 40: TNG library: Cannot open file spc2-traj.tng. /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c: 890 40: [ OK ] TngTest.CanOpenTngFile (0 ms) 40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 40: [----------] 2 tests from TngTest (0 ms total) 40: 40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (5 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (5 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 33 tests from 8 test cases ran. (11 ms total) 40: [ PASSED ] 33 tests. 40/54 Test #40: FileIOTests ......................... Passed 0.05 sec test 41 Start 41: SelectionUnitTests 41: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/SelectionUnitTests.xml" 41: Test timeout computed to be: 30 41: [==========] Running 192 tests from 11 test cases. 41: [----------] Global test environment set-up. 41: [----------] 1 test from IndexGroupTest 41: [ RUN ] IndexGroupTest.RemovesDuplicates 41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 41: [----------] 1 test from IndexGroupTest (0 ms total) 41: 41: [----------] 15 tests from IndexBlockTest 41: [ RUN ] IndexBlockTest.CreatesUnknownBlock 41: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 41: [ RUN ] IndexBlockTest.CreatesAtomBlock 41: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms) 41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesSingleBlock 41: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 41: [----------] 15 tests from IndexBlockTest (1 ms total) 41: 41: [----------] 11 tests from IndexMapTest 41: [ RUN ] IndexMapTest.InitializesAtomBlock 41: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 41: [ RUN ] IndexMapTest.InitializesMoleculeBlock 41: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 41: [ RUN ] IndexMapTest.MapsSingleBlock 41: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 41: [ RUN ] IndexMapTest.MapsResidueBlocks 41: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 41: [ RUN ] IndexMapTest.HandlesMultipleRequests 41: [ OK ] IndexMapTest.HandlesMultipleRequests (4 ms) 41: [----------] 11 tests from IndexMapTest (6 ms total) 41: 41: [----------] 3 tests from IndexGroupsAndNamesTest 41: [ RUN ] IndexGroupsAndNamesTest.containsNames 41: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 41: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 41: 41: [----------] 15 tests from NeighborhoodSearchTest 41: [ RUN ] NeighborhoodSearchTest.SimpleSearch 41: [ OK ] NeighborhoodSearchTest.SimpleSearch (16 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (15 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchBox 41: [ OK ] NeighborhoodSearchTest.GridSearchBox (3 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (10 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (5 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (3 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (41 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (4 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 41: [----------] 15 tests from NeighborhoodSearchTest (99 ms total) 41: 41: [----------] 12 tests from PositionCalculationTest 41: [ RUN ] PositionCalculationTest.ComputesAtomPositions 41: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionMask 41: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms) 41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 41: [----------] 12 tests from PositionCalculationTest (3 ms total) 41: 41: [----------] 29 tests from SelectionCollectionTest 41: [ RUN ] SelectionCollectionTest.HandlesNoSelections 41: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 41: [----------] 29 tests from SelectionCollectionTest (11 ms total) 41: 41: [----------] 14 tests from SelectionCollectionInteractiveTest 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms) 41: [----------] 14 tests from SelectionCollectionInteractiveTest (7 ms total) 41: 41: [----------] 66 tests from SelectionCollectionDataTest 41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResnr 41: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesChain 41: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMass 41: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesCharge 41: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBeta 41: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResname 41: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (4 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (2 ms) 41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (2 ms) 41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 41: [----------] 66 tests from SelectionCollectionDataTest (56 ms total) 41: 41: [----------] 17 tests from SelectionOptionTest 41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms) 41: [ RUN ] SelectionOptionTest.ChecksEmptySelections 41: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooManySelections 41: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesAdjuster 41: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms) 41: [----------] 17 tests from SelectionOptionTest (5 ms total) 41: 41: [----------] 9 tests from SelectionFileOptionTest 41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms) 41: [----------] 9 tests from SelectionFileOptionTest (3 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 192 tests from 11 test cases ran. (191 ms total) 41: [ PASSED ] 192 tests. 41/54 Test #41: SelectionUnitTests .................. Passed 0.21 sec test 42 Start 42: MdrunOutputTests 42: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunOutputTests.xml" 42: Test timeout computed to be: 600 42: [==========] Running 12 tests from 5 test cases. 42: [----------] Global test environment set-up. 42: [----------] 1 test from MdrunTest 42: [ RUN ] MdrunTest.WritesHelp 42: [ OK ] MdrunTest.WritesHelp (2 ms) 42: [----------] 1 test from MdrunTest (2 ms total) 42: 42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 42: Setting the LD random seed to -771754499 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.022 0.011 199.0 42: (ns/day) (hour/ns) 42: Performance: 15.828 1.516 42: Reading frame 0 time 0.000 42: # Atoms 6 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (161 ms) 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 42: Setting the LD random seed to 1879038963 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.019 0.009 198.8 42: (ns/day) (hour/ns) 42: Performance: 18.559 1.293 42: Reading frame 0 time 0.000 42: # Atoms 6 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (24 ms) 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 42: Setting the LD random seed to 1876406158 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.002 0.001 189.2 42: (ns/day) (hour/ns) 42: Performance: 177.990 0.135 42: Reading frame 0 time 0.000 42: # Atoms 3 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (22 ms) 42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (207 ms total) 42: 42: [----------] 2 tests from Argon12/OutputFiles 42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 42: that with the Verlet scheme, nstlist has no effect on the accuracy of 42: your simulation. 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: Setting nstcalcenergy (100) equal to nstenergy (4) 42: 42: Generated 1 of the 1 non-bonded parameter combinations 42: Excluding 1 bonded neighbours molecule type 'Argon' 42: Number of degrees of freedom in T-Coupling group System is 33.00 42: 42: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: NVE simulation: will use the initial temperature of 68.810 K for 42: determining the Verlet buffer size 42: 42: 42: There were 3 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'Argon' 42: 16 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.002 0.001 193.0 42: (ns/day) (hour/ns) 42: Performance: 1146.584 0.021 42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (15 ms) 42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 42: that with the Verlet scheme, nstlist has no effect on the accuracy of 42: your simulation. 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: Setting nstcalcenergy (100) equal to nstenergy (4) 42: 42: Generated 1 of the 1 non-bonded parameter combinations 42: Excluding 1 bonded neighbours molecule type 'Argon' 42: Number of degrees of freedom in T-Coupling group System is 33.00 42: 42: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: NVE simulation: will use the initial temperature of 68.810 K for 42: determining the Verlet buffer size 42: 42: 42: There were 3 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'Argon' 42: 16 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.019 0.010 199.0 42: (ns/day) (hour/ns) 42: Performance: 151.608 0.158 42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (23 ms) 42: [----------] 2 tests from Argon12/OutputFiles (38 ms total) 42: 42: [----------] 3 tests from MdrunCanWrite/Trajectories 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 42: Setting the LD random seed to 501179631 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.012 0.006 197.9 42: (ns/day) (hour/ns) 42: Performance: 100.691 0.238 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (21 ms) 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 42: Setting the LD random seed to 534559166 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.009 0.005 196.7 42: (ns/day) (hour/ns) 42: Performance: 126.842 0.189 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (23 ms) 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 42: Setting the LD random seed to -1912810473 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.005 0.003 194.9 42: (ns/day) (hour/ns) 42: Performance: 226.877 0.106 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (27 ms) 42: [----------] 3 tests from MdrunCanWrite/Trajectories (71 ms total) 42: 42: [----------] 3 tests from MdrunCanWrite/NptTrajectories 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 42: Setting the LD random seed to -538241546 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.002 0.001 191.1 42: (ns/day) (hour/ns) 42: Performance: 217.085 0.111 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (11 ms) 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 42: Setting the LD random seed to -289769161 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.002 0.001 190.7 42: (ns/day) (hour/ns) 42: Performance: 211.264 0.114 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (16 ms) 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 42: Setting the LD random seed to -559977657 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.002 0.001 191.1 42: (ns/day) (hour/ns) 42: Performance: 202.451 0.119 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (20 ms) 42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (47 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 12 tests from 5 test cases ran. (365 ms total) 42: [ PASSED ] 12 tests. 42/54 Test #42: MdrunOutputTests .................... Passed 0.38 sec test 43 Start 43: MdrunModulesTests 43: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunModulesTests.xml" 43: Test timeout computed to be: 600 43: [==========] Running 10 tests from 3 test cases. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from DensityFittingTest 43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 43: Setting the LD random seed to 1729609718 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = -3.8565400e+03 43: Maximum force = 2.8846870e+03 on atom 3 43: Norm of force = 1.0754448e+03 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data 43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (172 ms) 43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 43: Setting the LD random seed to 534707582 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = -2.7138666e+04 43: Maximum force = 4.3409717e+03 on atom 2 43: Norm of force = 1.2549793e+03 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data 43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (44 ms) 43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 43: 43: [WARNING] /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. 43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (8 ms) 43: [ RUN ] DensityFittingTest.CheckpointWorks 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 43: Setting nstcalcenergy (100) equal to nstenergy (2) 43: 43: Setting the LD random seed to 2113076839 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 43: NVE simulation: will use the initial temperature of 68.810 K for 43: determining the Verlet buffer size 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting mdrun 'Argon' 43: 2 steps, 0.0 ps. 43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.044 0.022 199.4 43: (ns/day) (hour/ns) 43: Performance: 11.653 2.059 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: 43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting mdrun 'Argon' 43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.002 0.001 189.9 43: (ns/day) (hour/ns) 43: Performance: 498.333 0.048 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (35 ms) 43: [----------] 4 tests from DensityFittingTest (259 ms total) 43: 43: [----------] 4 tests from MimicTest 43: [ RUN ] MimicTest.OneQuantumMol 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -570431781 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 23 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.000 0.000 187.0 43: (ns/day) (hour/ns) 43: Performance: 351.151 0.068 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.OneQuantumMol (13 ms) 43: [ RUN ] MimicTest.AllQuantumMol 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to 1203765134 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 21 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.000 0.000 186.8 43: (ns/day) (hour/ns) 43: Performance: 391.348 0.061 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.AllQuantumMol (10 ms) 43: [ RUN ] MimicTest.TwoQuantumMol 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to 2145384668 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 98 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.025 0.012 199.7 43: (ns/day) (hour/ns) 43: Performance: 7.015 3.421 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.TwoQuantumMol (22 ms) 43: [ RUN ] MimicTest.BondCuts 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -39124999 43: Generated 2211 of the 2211 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 2211 of the 2211 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 43: Number of degrees of freedom in T-Coupling group rest is 66.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: NVE simulation: will use the initial temperature of 300.368 K for 43: determining the Verlet buffer size 43: 43: 43: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/ala.gro' 43: 43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 19 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.000 191.2 43: (ns/day) (hour/ns) 43: Performance: 194.727 0.123 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.BondCuts (49 ms) 43: [----------] 4 tests from MimicTest (94 ms total) 43: 43: [----------] 2 tests from WithIntegrator/ImdTest 43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 43: Setting the LD random seed to 2012921647 43: Generated 20503 of the 20503 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 1 43: Generated 17396 of the 20503 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Glycine' 43: 43: NOTE 1 [file glycine_vacuo.top, line 12]: 43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 43: the time step of 2.0e-03 ps. 43: Maybe you forgot to change the constraints mdp option. 43: 43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 43: Number of degrees of freedom in T-Coupling group System is 27.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34 43: 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: IMD: Enabled. This simulation will accept incoming IMD connections. 43: IMD: Pulling from IMD remote is enabled (-imdpull). 43: IMD: Setting port for connection requests to 0. 43: IMD: Setting up incoming socket. 43: IMD: Listening for IMD connection on port 43175. 43: IMD: -imdwait not set, starting simulation. 43: starting mdrun 'Glycine' 43: 2 steps, 0.0 ps. 43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.003 0.001 190.2 43: (ns/day) (hour/ns) 43: Performance: 377.684 0.064 43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (337 ms) 43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 43: apply to steep. 43: 43: Setting the LD random seed to -1090552110 43: Generated 20503 of the 20503 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 1 43: Generated 17396 of the 20503 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Glycine' 43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 43: Number of degrees of freedom in T-Coupling group System is 27.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: IMD: Enabled. This simulation will accept incoming IMD connections. 43: IMD: Pulling from IMD remote is enabled (-imdpull). 43: IMD: Setting port for connection requests to 0. 43: IMD: Setting up incoming socket. 43: IMD: Listening for IMD connection on port 57805. 43: IMD: -imdwait not set, starting simulation. 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = 1.1977063e+03 43: Maximum force = 1.7794877e+04 on atom 9 43: Norm of force = 7.8732901e+03 43: This run will generate roughly 0 Mb of data 43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (247 ms) 43: [----------] 2 tests from WithIntegrator/ImdTest (584 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 10 tests from 3 test cases ran. (937 ms total) 43: [ PASSED ] 10 tests. 43/54 Test #43: MdrunModulesTests ................... Passed 0.95 sec test 44 Start 44: MdrunIOTests 44: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunIOTests.xml" 44: Test timeout computed to be: 600 44: [==========] Running 51 tests from 9 test cases. 44: [----------] Global test environment set-up. 44: [----------] 3 tests from GromppTest 44: [ RUN ] GromppTest.EmptyMdpFileWorks 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -147465 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 12.00 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.EmptyMdpFileWorks (5 ms) 44: [ RUN ] GromppTest.SimulatedAnnealingWorks 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -268845587 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Simulated annealing for group rest: Periodic, 4 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 2.0 320.0 44: 4.0 320.0 44: 6.0 298.0 44: Number of degrees of freedom in T-Coupling group rest is 12.00 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.SimulatedAnnealingWorks (4 ms) 44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to 1952129023 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Simulated annealing for group Methanol: Single, 3 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 3.0 280.0 44: 6.0- 270.0 44: Simulated annealing for group SOL: Periodic, 4 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 2.0 320.0 44: 4.0 320.0 44: 6.0 298.0 44: Number of degrees of freedom in T-Coupling group Methanol is 7.20 44: Number of degrees of freedom in T-Coupling group SOL is 4.80 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (6 ms) 44: [----------] 3 tests from GromppTest (15 ms total) 44: 44: [----------] 6 tests from MdrunTerminationTest 44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 44: Setting the LD random seed to -624955395 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 193.3 44: (ns/day) (hour/ns) 44: Performance: 110.294 0.218 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.001 0.001 185.5 44: (ns/day) (hour/ns) 44: Performance: 380.660 0.063 44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (180 ms) 44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 44: Setting the LD random seed to -302516373 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 1, rlist from 1.024 to 1 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 100 steps, 0.1 ps. 44: 44: Step 5: Run time exceeded 0.000 hours, will terminate the run within 2 steps 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: NOTE: 14 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.2 44: (ns/day) (hour/ns) 44: Performance: 591.447 0.041 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 102 44: Writing statusfile with starting step 0 and length 102 steps... 44: time 0.000 and length 0.102 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 102 steps, 0.1 ps (continuing from step 6, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.030 0.015 199.2 44: (ns/day) (hour/ns) 44: Performance: 553.107 0.043 44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (32 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 44: Setting the LD random seed to 1384120303 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 188.1 44: (ns/day) (hour/ns) 44: Performance: 297.283 0.081 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.034 0.017 199.7 44: (ns/day) (hour/ns) 44: Performance: 15.256 1.573 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 6 44: Writing statusfile with starting step 0 and length 6 steps... 44: time 0.000 and length 0.006 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.025 0.012 199.4 44: (ns/day) (hour/ns) 44: Performance: 20.936 1.146 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 8 44: Writing statusfile with starting step 0 and length 8 steps... 44: time 0.000 and length 0.008 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 195.1 44: (ns/day) (hour/ns) 44: Performance: 309.117 0.078 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: NOTE: 26 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.000 0.000 178.8 44: (ns/day) (hour/ns) 44: Performance: 511.847 0.047 44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (66 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 44: Setting the LD random seed to -37748817 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 187.3 44: (ns/day) (hour/ns) 44: Performance: 298.262 0.080 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.025 0.013 198.8 44: (ns/day) (hour/ns) 44: Performance: 34.206 0.702 44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (32 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 44: Setting the LD random seed to -751304713 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 188.2 44: (ns/day) (hour/ns) 44: Performance: 312.134 0.077 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (18 ms) 44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 44: Setting the LD random seed to 2013265406 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 188.2 44: (ns/day) (hour/ns) 44: Performance: 304.357 0.079 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 193.7 44: (ns/day) (hour/ns) 44: Performance: 334.101 0.072 44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (50 ms) 44: [----------] 6 tests from MdrunTerminationTest (378 ms total) 44: 44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 190.5 44: (ns/day) (hour/ns) 44: Performance: 1054.174 0.023 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.4 44: (ns/day) (hour/ns) 44: Performance: 751.149 0.032 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 184.2 44: (ns/day) (hour/ns) 44: Performance: 734.239 0.033 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (32 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 195.9 44: (ns/day) (hour/ns) 44: Performance: 952.620 0.025 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 196.8 44: (ns/day) (hour/ns) 44: Performance: 572.392 0.042 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 196.7 44: (ns/day) (hour/ns) 44: Performance: 655.444 0.037 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (33 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 193.1 44: (ns/day) (hour/ns) 44: Performance: 1114.434 0.022 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.3 44: (ns/day) (hour/ns) 44: Performance: 747.020 0.032 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 199.0 44: (ns/day) (hour/ns) 44: Performance: 59.517 0.403 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (51 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.6 44: (ns/day) (hour/ns) 44: Performance: 1103.061 0.022 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.3 44: (ns/day) (hour/ns) 44: Performance: 728.336 0.033 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 199.1 44: (ns/day) (hour/ns) 44: Performance: 59.265 0.405 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (48 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.0 44: (ns/day) (hour/ns) 44: Performance: 1066.585 0.023 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.8 44: (ns/day) (hour/ns) 44: Performance: 684.899 0.035 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 198.9 44: (ns/day) (hour/ns) 44: Performance: 60.245 0.398 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (48 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 196.6 44: (ns/day) (hour/ns) 44: Performance: 826.814 0.029 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 196.4 44: (ns/day) (hour/ns) 44: Performance: 592.030 0.041 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 199.4 44: (ns/day) (hour/ns) 44: Performance: 59.509 0.403 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (48 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.3 44: (ns/day) (hour/ns) 44: Performance: 1004.172 0.024 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: NOTE: 28 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.227 0.113 199.9 44: (ns/day) (hour/ns) 44: Performance: 6.853 3.502 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.016 0.008 198.7 44: (ns/day) (hour/ns) 44: Performance: 96.468 0.249 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (204 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 193.0 44: (ns/day) (hour/ns) 44: Performance: 986.168 0.024 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.2 44: (ns/day) (hour/ns) 44: Performance: 689.971 0.035 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: NOTE: 79 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 198.1 44: (ns/day) (hour/ns) 44: Performance: 152.023 0.158 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (33 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.014 0.007 197.7 44: (ns/day) (hour/ns) 44: Performance: 203.239 0.118 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 196.7 44: (ns/day) (hour/ns) 44: Performance: 150.939 0.159 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 195.5 44: (ns/day) (hour/ns) 44: Performance: 198.315 0.121 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (78 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.005 197.0 44: (ns/day) (hour/ns) 44: Performance: 268.038 0.090 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 193.4 44: (ns/day) (hour/ns) 44: Performance: 335.717 0.071 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.003 157.5 44: (ns/day) (hour/ns) 44: Performance: 282.258 0.085 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (58 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 195.6 44: (ns/day) (hour/ns) 44: Performance: 410.105 0.059 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 194.3 44: (ns/day) (hour/ns) 44: Performance: 279.644 0.086 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 194.5 44: (ns/day) (hour/ns) 44: Performance: 300.876 0.080 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (85 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.005 196.3 44: (ns/day) (hour/ns) 44: Performance: 314.750 0.076 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 194.4 44: (ns/day) (hour/ns) 44: Performance: 299.274 0.080 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 195.2 44: (ns/day) (hour/ns) 44: Performance: 259.322 0.093 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (92 ms) 44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (810 ms total) 44: 44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.017 0.009 197.6 44: (ns/day) (hour/ns) 44: Performance: 171.633 0.140 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 193.0 44: (ns/day) (hour/ns) 44: Performance: 335.752 0.071 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 193.8 44: (ns/day) (hour/ns) 44: Performance: 272.700 0.088 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (60 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 198.3 44: (ns/day) (hour/ns) 44: Performance: 299.888 0.080 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 197.7 44: (ns/day) (hour/ns) 44: Performance: 242.112 0.099 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: NOTE: 53 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 198.4 44: (ns/day) (hour/ns) 44: Performance: 155.591 0.154 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (57 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: NOTE: 15 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.005 176.9 44: (ns/day) (hour/ns) 44: Performance: 325.252 0.074 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 192.7 44: (ns/day) (hour/ns) 44: Performance: 347.744 0.069 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 192.4 44: (ns/day) (hour/ns) 44: Performance: 329.743 0.073 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (95 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.0 44: (ns/day) (hour/ns) 44: Performance: 360.121 0.067 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 194.3 44: (ns/day) (hour/ns) 44: Performance: 265.054 0.091 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 193.2 44: (ns/day) (hour/ns) 44: Performance: 288.372 0.083 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (76 ms) 44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (288 ms total) 44: 44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.6 44: (ns/day) (hour/ns) 44: Performance: 1122.353 0.021 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.9 44: (ns/day) (hour/ns) 44: Performance: 776.361 0.031 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.7 44: (ns/day) (hour/ns) 44: Performance: 615.840 0.039 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (21 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.7 44: (ns/day) (hour/ns) 44: Performance: 1113.226 0.022 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.4 44: (ns/day) (hour/ns) 44: Performance: 716.024 0.034 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.0 44: (ns/day) (hour/ns) 44: Performance: 756.726 0.032 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (20 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 188.1 44: (ns/day) (hour/ns) 44: Performance: 1017.439 0.024 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.8 44: (ns/day) (hour/ns) 44: Performance: 781.945 0.031 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.2 44: (ns/day) (hour/ns) 44: Performance: 758.486 0.032 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (20 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 193.1 44: (ns/day) (hour/ns) 44: Performance: 1048.077 0.023 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.2 44: (ns/day) (hour/ns) 44: Performance: 735.730 0.033 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 190.3 44: (ns/day) (hour/ns) 44: Performance: 472.748 0.051 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (29 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 196.2 44: (ns/day) (hour/ns) 44: Performance: 661.576 0.036 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 196.1 44: (ns/day) (hour/ns) 44: Performance: 606.902 0.040 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 196.4 44: (ns/day) (hour/ns) 44: Performance: 619.231 0.039 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (42 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.019 0.010 198.9 44: (ns/day) (hour/ns) 44: Performance: 152.373 0.158 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 192.5 44: (ns/day) (hour/ns) 44: Performance: 633.176 0.038 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 192.0 44: (ns/day) (hour/ns) 44: Performance: 676.798 0.035 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (33 ms) 44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (165 ms total) 44: 44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.005 198.1 44: (ns/day) (hour/ns) 44: Performance: 267.375 0.090 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.4 44: (ns/day) (hour/ns) 44: Performance: 731.276 0.033 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.7 44: (ns/day) (hour/ns) 44: Performance: 700.342 0.034 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (35 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.0 44: (ns/day) (hour/ns) 44: Performance: 1023.865 0.023 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.8 44: (ns/day) (hour/ns) 44: Performance: 793.357 0.030 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.1 44: (ns/day) (hour/ns) 44: Performance: 747.534 0.032 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (20 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.1 44: (ns/day) (hour/ns) 44: Performance: 976.787 0.025 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.8 44: (ns/day) (hour/ns) 44: Performance: 701.396 0.034 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.0 44: (ns/day) (hour/ns) 44: Performance: 692.902 0.035 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (20 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 197.0 44: (ns/day) (hour/ns) 44: Performance: 868.913 0.028 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 196.5 44: (ns/day) (hour/ns) 44: Performance: 668.064 0.036 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 196.4 44: (ns/day) (hour/ns) 44: Performance: 613.754 0.039 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (20 ms) 44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (95 ms total) 44: 44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.3 44: (ns/day) (hour/ns) 44: Performance: 1118.278 0.021 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 188.0 44: (ns/day) (hour/ns) 44: Performance: 675.117 0.036 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.8 44: (ns/day) (hour/ns) 44: Performance: 778.399 0.031 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (20 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.0 44: (ns/day) (hour/ns) 44: Performance: 1109.417 0.022 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.0 44: (ns/day) (hour/ns) 44: Performance: 764.352 0.031 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.6 44: (ns/day) (hour/ns) 44: Performance: 738.730 0.032 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (21 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 192.1 44: (ns/day) (hour/ns) 44: Performance: 1156.051 0.021 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.5 44: (ns/day) (hour/ns) 44: Performance: 771.038 0.031 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.3 44: (ns/day) (hour/ns) 44: Performance: 781.008 0.031 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (18 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 192.0 44: (ns/day) (hour/ns) 44: Performance: 1147.011 0.021 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.6 44: (ns/day) (hour/ns) 44: Performance: 713.674 0.034 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.1 44: (ns/day) (hour/ns) 44: Performance: 288.067 0.083 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (21 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: 44: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Using Berendsen pressure coupling invalidates the true ensemble for the 44: thermostat 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: There was 1 warning 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: 44: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Using Berendsen pressure coupling invalidates the true ensemble for the 44: thermostat 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: There was 1 warning 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.2 44: (ns/day) (hour/ns) 44: Performance: 1087.483 0.022 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.9 44: (ns/day) (hour/ns) 44: Performance: 814.965 0.029 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 196.6 44: (ns/day) (hour/ns) 44: Performance: 259.963 0.092 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (20 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 194.1 44: (ns/day) (hour/ns) 44: Performance: 833.188 0.029 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.3 44: (ns/day) (hour/ns) 44: Performance: 768.313 0.031 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.0 44: (ns/day) (hour/ns) 44: Performance: 789.134 0.030 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (17 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.9 44: (ns/day) (hour/ns) 44: Performance: 1014.925 0.024 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.7 44: (ns/day) (hour/ns) 44: Performance: 727.200 0.033 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 195.2 44: (ns/day) (hour/ns) 44: Performance: 354.010 0.068 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (18 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 194.9 44: (ns/day) (hour/ns) 44: Performance: 706.328 0.034 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 153.8 44: (ns/day) (hour/ns) 44: Performance: 568.006 0.042 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.5 44: (ns/day) (hour/ns) 44: Performance: 755.674 0.032 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (17 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 197.0 44: (ns/day) (hour/ns) 44: Performance: 876.828 0.027 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 195.5 44: (ns/day) (hour/ns) 44: Performance: 674.001 0.036 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 197.5 44: (ns/day) (hour/ns) 44: Performance: 387.996 0.062 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (19 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms) 44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (172 ms total) 44: 44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 195.7 44: (ns/day) (hour/ns) 44: Performance: 592.593 0.040 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.3 44: (ns/day) (hour/ns) 44: Performance: 489.199 0.049 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 192.0 44: (ns/day) (hour/ns) 44: Performance: 640.513 0.037 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (18 ms) 44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (18 ms total) 44: 44: [----------] 3 tests from Checking/InitialConstraintsTest 44: [ RUN ] Checking/InitialConstraintsTest.Works/0 44: Setting the LD random seed to -1078214793 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 188.6 44: (ns/day) (hour/ns) 44: Performance: 165.550 0.145 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (7 ms) 44: [ RUN ] Checking/InitialConstraintsTest.Works/1 44: Setting the LD random seed to -1053337 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 195.3 44: (ns/day) (hour/ns) 44: Performance: 135.472 0.177 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (7 ms) 44: [ RUN ] Checking/InitialConstraintsTest.Works/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: Integrator method md-vv-avek is implemented primarily for validation 44: purposes; for molecular dynamics, you should probably be using md or md-vv 44: 44: Setting the LD random seed to -11356425 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 185.2 44: (ns/day) (hour/ns) 44: Performance: 202.282 0.119 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (7 ms) 44: [----------] 3 tests from Checking/InitialConstraintsTest (21 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 51 tests from 9 test cases ran. (1962 ms total) 44: [ PASSED ] 51 tests. 44/54 Test #44: MdrunIOTests ........................ Passed 1.98 sec test 45 Start 45: MdrunTests 45: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunTests.xml" 45: Test timeout computed to be: 600 45: [==========] Running 12 tests from 5 test cases. 45: [----------] Global test environment set-up. 45: [----------] 1 test from DispersionCorrectionTest 45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to -209731933 45: Generated 2145 of the 2145 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 2145 of the 2145 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 45: Cleaning up constraints and constant bonded interactions with virtual sites 45: Converted 3 Bonds with virtual sites to connections, 7 left 45: Removed 18 Angles with virtual sites, 21 left 45: Removed 10 Proper Dih.s with virtual sites, 44 left 45: Converted 12 Constraints with virtual sites to connections, 0 left 45: Number of degrees of freedom in T-Coupling group System is 30.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: There are 9 non-linear virtual site constructions. Their contribution to 45: the energy error is approximated. In most cases this does not affect the 45: error significantly. 45: 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Changing nstlist from 10 to 50, rlist from 1.016 to 1.167 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Alanine dipeptide in vacuo' 45: 200 steps, 0.4 ps. 45: turning H bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.092 0.046 199.6 45: (ns/day) (hour/ns) 45: Performance: 755.018 0.032 45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (232 ms) 45: [----------] 1 test from DispersionCorrectionTest (232 ms total) 45: 45: [----------] 1 test from OriresTest 45: [ RUN ] OriresTest.OriresCanRun 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to -543762690 45: Generated 2145 of the 2145 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 2145 of the 2145 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 518.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: 45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 45: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 45: 10 steps, 0.0 ps. 45: turning H bonds into constraints... 45: turning H bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.025 0.012 198.5 45: (ns/day) (hour/ns) 45: Performance: 152.206 0.158 45: [ OK ] OriresTest.OriresCanRun (288 ms) 45: [----------] 1 test from OriresTest (288 ms total) 45: 45: [----------] 3 tests from PmeTest 45: [ RUN ] PmeTest.ReproducesEnergies 45: Setting the LD random seed to -25762 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group rest is 12.00 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 45: NVE simulation: will use the initial temperature of 1046.791 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.059 0.030 199.5 45: (ns/day) (hour/ns) 45: Performance: 61.476 0.390 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.058 0.029 199.4 45: (ns/day) (hour/ns) 45: Performance: 62.090 0.387 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.042 0.021 199.3 45: (ns/day) (hour/ns) 45: Performance: 86.071 0.279 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (410 ms) 45: [ RUN ] PmeTest.ScalesTheBox 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -33624329 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group rest is 12.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: NVE simulation: will use the initial temperature of 1046.791 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 0 steps, 0.0 ps. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.002 0.001 184.4 45: (ns/day) (hour/ns) 45: Performance: 102.254 0.235 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 45: This run will generate roughly 0 Mb of data 45: [ OK ] PmeTest.ScalesTheBox (17 ms) 45: [ RUN ] PmeTest.ScalesTheBoxWithWalls 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -9052241 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Searching the wall atom type(s) 45: Number of degrees of freedom in T-Coupling group rest is 13.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: NVE simulation: will use the initial temperature of 966.268 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 0 steps, 0.0 ps. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.005 0.002 191.7 45: (ns/day) (hour/ns) 45: Performance: 36.664 0.655 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 45: This run will generate roughly 0 Mb of data 45: [ OK ] PmeTest.ScalesTheBoxWithWalls (599 ms) 45: [----------] 3 tests from PmeTest (1027 ms total) 45: 45: [----------] 1 test from CompelTest 45: [ RUN ] CompelTest.SwapCanRun 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to 402254623 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Protein' 45: Excluding 3 bonded neighbours molecule type 'OCT' 45: Excluding 1 bonded neighbours molecule type 'NA' 45: Excluding 1 bonded neighbours molecule type 'CL' 45: Excluding 3 bonded neighbours molecule type 'Protein' 45: Excluding 3 bonded neighbours molecule type 'OCT' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Split0 group 'Ch0' contains 83 atoms. 45: Split1 group 'Ch1' contains 83 atoms. 45: Solvent group 'SOL' contains 11931 atoms. 45: Swap group 'NA+' contains 19 atoms. 45: Swap group 'CL-' contains 19 atoms. 45: Number of degrees of freedom in T-Coupling group System is 27869.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: Removing center of mass motion in the presence of position restraints 45: might cause artifacts. When you are using position restraints to 45: equilibrate a macro-molecule, the artifacts are usually negligible. 45: 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: SWAP: Determining initial numbers of ions per compartment. 45: SWAP: Setting pointers for checkpoint writing 45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 45: starting mdrun 'Channel_coco in octane membrane' 45: 2 steps, 0.0 ps. 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 1 Mb of data 45: 45: Writing final coordinates. 45: 45: NOTE: 35 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.789 0.394 199.9 45: (ns/day) (hour/ns) 45: Performance: 3.286 7.304 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: SWAP: Setting pointers for checkpoint writing 45: SWAP: Copying channel fluxes from checkpoint file data 45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 45: starting mdrun 'Channel_coco in octane membrane' 45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 45: 45: Writing final coordinates. 45: 45: NOTE: 27 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.401 0.201 199.9 45: (ns/day) (hour/ns) 45: Performance: 6.464 3.713 45: [ OK ] CompelTest.SwapCanRun (1514 ms) 45: [----------] 1 test from CompelTest (1514 ms total) 45: 45: [----------] 6 tests from BondedInteractionsTest 45: [ RUN ] BondedInteractionsTest.NormalBondWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to 2137831821 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 2 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 21 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.000 0.000 185.2 45: (ns/day) (hour/ns) 45: Performance: 377.881 0.064 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalBondWorks (7 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -4220969 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 2 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 19 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.000 0.000 183.6 45: (ns/day) (hour/ns) 45: Performance: 390.925 0.061 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (19 ms) 45: [ RUN ] BondedInteractionsTest.NormalAngleWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -1409286822 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 14 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.000 0.000 163.6 45: (ns/day) (hour/ns) 45: Performance: 335.234 0.072 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalAngleWorks (13 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -73482945 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 26 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.000 0.000 185.9 45: (ns/day) (hour/ns) 45: Performance: 394.328 0.061 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (10 ms) 45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -808847441 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 17 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.000 0.000 184.2 45: (ns/day) (hour/ns) 45: Performance: 455.261 0.053 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (14 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to 2125798387 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 17 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.000 0.000 184.1 45: (ns/day) (hour/ns) 45: Performance: 400.429 0.060 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (17 ms) 45: [----------] 6 tests from BondedInteractionsTest (80 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 12 tests from 5 test cases ran. (3143 ms total) 45: [ PASSED ] 12 tests. 45: 45: YOU HAVE 12 DISABLED TESTS 45: 45/54 Test #45: MdrunTests .......................... Passed 3.17 sec test 46 Start 46: MdrunNonIntegratorTests 46: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 46: Test timeout computed to be: 600 46: [==========] Running 58 tests from 5 test cases. 46: [----------] Global test environment set-up. 46: [----------] 1 test from NonbondedBenchTest 46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 46: SIMD width: 4 46: System size: 3000 atoms 46: Cut-off radius: 1 nm 46: Number of threads: 1 46: Number of iterations: 1 46: Compute energies: no 46: Ewald excl. corr.: analytical 46: 46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 46: total useful 46: Ewald all geom. 4xM 18.318 18.3176 0.0650 0.0344 46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (26 ms) 46: [----------] 1 test from NonbondedBenchTest (27 ms total) 46: 46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -4.7990971e+01 46: Maximum force = 1.8629765e+02 on atom 13 46: Norm of force = 8.7721828e+01 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (643 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 3.02331e+02 on atom 3 46: F-Norm = 1.18024e+02 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -5.5862602e+01 46: Maximum force = 4.2725583e+02 on atom 13 46: Norm of force = 1.8452307e+02 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (593 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 22.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 3.1937714e+02 46: Maximum force = 9.9988643e+03 on atom 9 46: Norm of force = 4.6166996e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (156 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: 46: NOTE 3 [file glycine_vacuo.top, line 12]: 46: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 46: 46: Number of degrees of freedom in T-Coupling group System is 22.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 2.41575e+04 on atom 10 46: F-Norm = 1.18451e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 1.5174426e+02 46: Maximum force = 7.4208862e+03 on atom 9 46: Norm of force = 3.5692992e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (155 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -1.5698431e+02 46: Maximum force = 4.5699701e+02 on atom 17 46: Norm of force = 1.8327127e+02 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (22 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: 46: NOTE 4 [file unknown]: 46: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 1.06802e+03 on atom 28 46: F-Norm = 4.26922e+02 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -1.6941113e+02 46: Maximum force = 2.1829993e+02 on atom 17 46: Norm of force = 7.9203658e+01 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (28 ms) 46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1597 ms total) 46: 46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents converged to Fmax < 10 in 1 steps 46: Potential Energy = -9.7425687e-01 46: Maximum force = 4.0132279e+00 on atom 1 46: Norm of force = 1.6383933e+00 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (13 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 4.01323e+00 on atom 1 46: F-Norm = 1.63839e+00 46: 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 46: Potential Energy = -9.9064195e-01 46: Maximum force = 2.5781672e+00 on atom 1 46: Norm of force = 1.0525324e+00 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (6 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: 46: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: 46: There was 1 warning 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Low-Memory BFGS Minimizer: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: Using 10 BFGS correction steps. 46: 46: F-max = 4.01323e+00 on atom 1 46: F-Norm = 1.63839e+00 46: 46: 46: writing lowest energy coordinates. 46: 46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 46: Potential Energy = -9.9064195e-01 46: Maximum force = 2.5781672e+00 on atom 1 46: Norm of force = 1.0525324e+00 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (10 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 3.1939700e+02 46: Maximum force = 9.9704248e+03 on atom 9 46: Norm of force = 4.6227540e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (153 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 2.41672e+04 on atom 10 46: F-Norm = 1.19357e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 1.5625757e+02 46: Maximum force = 7.5018242e+03 on atom 9 46: Norm of force = 3.6139019e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (152 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: 46: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: 46: There was 1 warning 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Low-Memory BFGS Minimizer: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: Using 10 BFGS correction steps. 46: 46: F-max = 2.41672e+04 on atom 10 46: F-Norm = 1.19357e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 5.6111731e+02 46: Maximum force = 1.2685497e+04 on atom 10 46: Norm of force = 6.0643635e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (152 ms) 46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (486 ms total) 46: 46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 68.810 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.018 0.009 198.8 46: (ns/day) (hour/ns) 46: Performance: 162.275 0.148 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 46: 46: trr version: GMX_trn_file (single precision) 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 25 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.000 194.4 46: (ns/day) (hour/ns) 46: Performance: 3071.084 0.008 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (18 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 68.810 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.2 46: (ns/day) (hour/ns) 46: Performance: 950.269 0.025 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 22 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 193.9 46: (ns/day) (hour/ns) 46: Performance: 2868.060 0.008 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (19 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 192.6 46: (ns/day) (hour/ns) 46: Performance: 1125.428 0.021 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 22 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.000 193.9 46: (ns/day) (hour/ns) 46: Performance: 2968.961 0.008 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (16 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 192.3 46: (ns/day) (hour/ns) 46: Performance: 1081.375 0.022 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 22 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.000 193.9 46: (ns/day) (hour/ns) 46: Performance: 3285.650 0.007 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (16 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: NVE simulation: will use the initial temperature of 398.997 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 196.0 46: (ns/day) (hour/ns) 46: Performance: 519.574 0.046 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 23 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.2 46: (ns/day) (hour/ns) 46: Performance: 2649.718 0.009 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (540 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: NVE simulation: will use the initial temperature of 398.997 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 197.1 46: (ns/day) (hour/ns) 46: Performance: 751.475 0.032 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 23 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 192.3 46: (ns/day) (hour/ns) 46: Performance: 2207.307 0.011 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (685 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.0 46: (ns/day) (hour/ns) 46: Performance: 971.702 0.025 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 24 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.4 46: (ns/day) (hour/ns) 46: Performance: 2553.085 0.009 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (655 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.3 46: (ns/day) (hour/ns) 46: Performance: 899.488 0.027 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 19 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.1 46: (ns/day) (hour/ns) 46: Performance: 2449.540 0.010 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (604 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: NVE simulation: will use the initial temperature of 456.887 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 6 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 195.4 46: (ns/day) (hour/ns) 46: Performance: 468.771 0.051 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 18 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.6 46: (ns/day) (hour/ns) 46: Performance: 1696.199 0.014 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (37 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: NVE simulation: will use the initial temperature of 456.887 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 6 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.003 195.5 46: (ns/day) (hour/ns) 46: Performance: 435.255 0.055 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 16 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 193.4 46: (ns/day) (hour/ns) 46: Performance: 1409.424 0.017 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (40 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 194.9 46: (ns/day) (hour/ns) 46: Performance: 442.127 0.054 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 195.9 46: (ns/day) (hour/ns) 46: Performance: 1199.960 0.020 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (52 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.008 0.004 196.7 46: (ns/day) (hour/ns) 46: Performance: 347.546 0.069 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 17 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.4 46: (ns/day) (hour/ns) 46: Performance: 1447.848 0.017 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (47 ms) 46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2729 ms total) 46: 46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.005 0.003 193.0 46: (ns/day) (hour/ns) 46: Performance: 534.542 0.045 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.7 46: (ns/day) (hour/ns) 46: Performance: 932.011 0.026 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (37 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 194.9 46: (ns/day) (hour/ns) 46: Performance: 456.374 0.053 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.018 0.009 198.9 46: (ns/day) (hour/ns) 46: Performance: 159.932 0.150 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (40 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.021 0.010 197.8 46: (ns/day) (hour/ns) 46: Performance: 140.585 0.171 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.0 46: (ns/day) (hour/ns) 46: Performance: 1131.838 0.021 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (36 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.005 0.003 194.1 46: (ns/day) (hour/ns) 46: Performance: 541.734 0.044 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 195.3 46: (ns/day) (hour/ns) 46: Performance: 1145.731 0.021 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (35 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 193.7 46: (ns/day) (hour/ns) 46: Performance: 512.103 0.047 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.4 46: (ns/day) (hour/ns) 46: Performance: 1318.338 0.018 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (33 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.005 0.003 193.8 46: (ns/day) (hour/ns) 46: Performance: 547.560 0.044 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 88 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.019 0.009 198.7 46: (ns/day) (hour/ns) 46: Performance: 156.894 0.153 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (55 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.023 0.012 198.2 46: (ns/day) (hour/ns) 46: Performance: 127.372 0.188 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 16 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.2 46: (ns/day) (hour/ns) 46: Performance: 1179.287 0.020 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (40 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.003 194.1 46: (ns/day) (hour/ns) 46: Performance: 429.669 0.056 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.018 0.009 198.8 46: (ns/day) (hour/ns) 46: Performance: 158.917 0.151 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (41 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.023 0.011 198.2 46: (ns/day) (hour/ns) 46: Performance: 128.969 0.186 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.7 46: (ns/day) (hour/ns) 46: Performance: 1143.816 0.021 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (39 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.003 194.2 46: (ns/day) (hour/ns) 46: Performance: 426.486 0.056 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.019 0.009 198.6 46: (ns/day) (hour/ns) 46: Performance: 155.116 0.155 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (41 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.022 0.011 197.8 46: (ns/day) (hour/ns) 46: Performance: 133.842 0.179 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 16 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.1 46: (ns/day) (hour/ns) 46: Performance: 1092.885 0.022 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (39 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.024 0.012 199.0 46: (ns/day) (hour/ns) 46: Performance: 123.878 0.194 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.0 46: (ns/day) (hour/ns) 46: Performance: 1259.578 0.019 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (41 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.003 197.7 46: (ns/day) (hour/ns) 46: Performance: 426.930 0.056 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.018 0.009 198.9 46: (ns/day) (hour/ns) 46: Performance: 158.631 0.151 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (39 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.003 197.4 46: (ns/day) (hour/ns) 46: Performance: 433.478 0.055 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 16 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.2 46: (ns/day) (hour/ns) 46: Performance: 1188.157 0.020 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (33 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.023 0.012 199.1 46: (ns/day) (hour/ns) 46: Performance: 127.586 0.188 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.0 46: (ns/day) (hour/ns) 46: Performance: 1319.185 0.018 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (38 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 197.6 46: (ns/day) (hour/ns) 46: Performance: 470.634 0.051 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 193.8 46: (ns/day) (hour/ns) 46: Performance: 1010.762 0.024 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (33 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 197.5 46: (ns/day) (hour/ns) 46: Performance: 405.409 0.059 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.019 0.009 198.5 46: (ns/day) (hour/ns) 46: Performance: 156.028 0.154 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (40 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.023 0.012 199.0 46: (ns/day) (hour/ns) 46: Performance: 125.310 0.192 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 193.9 46: (ns/day) (hour/ns) 46: Performance: 1203.241 0.020 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (38 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.008 0.004 197.4 46: (ns/day) (hour/ns) 46: Performance: 369.917 0.065 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.7 46: (ns/day) (hour/ns) 46: Performance: 1196.697 0.020 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (29 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.003 197.8 46: (ns/day) (hour/ns) 46: Performance: 421.266 0.057 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.8 46: (ns/day) (hour/ns) 46: Performance: 915.257 0.026 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (29 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 197.4 46: (ns/day) (hour/ns) 46: Performance: 399.209 0.060 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 192.9 46: (ns/day) (hour/ns) 46: Performance: 1337.805 0.018 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (29 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 197.8 46: (ns/day) (hour/ns) 46: Performance: 399.028 0.060 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 190.4 46: (ns/day) (hour/ns) 46: Performance: 1147.011 0.021 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (30 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 194.2 46: (ns/day) (hour/ns) 46: Performance: 445.290 0.054 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.6 46: (ns/day) (hour/ns) 46: Performance: 1097.363 0.022 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (49 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 197.6 46: (ns/day) (hour/ns) 46: Performance: 204.352 0.117 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.5 46: (ns/day) (hour/ns) 46: Performance: 871.125 0.028 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (56 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.023 0.012 198.2 46: (ns/day) (hour/ns) 46: Performance: 125.429 0.191 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.2 46: (ns/day) (hour/ns) 46: Performance: 933.848 0.026 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (64 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.022 0.011 197.7 46: (ns/day) (hour/ns) 46: Performance: 133.087 0.180 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.1 46: (ns/day) (hour/ns) 46: Performance: 1083.086 0.022 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (62 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.003 195.0 46: (ns/day) (hour/ns) 46: Performance: 430.720 0.056 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.7 46: (ns/day) (hour/ns) 46: Performance: 1002.375 0.024 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (51 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 193.9 46: (ns/day) (hour/ns) 46: Performance: 394.783 0.061 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.4 46: (ns/day) (hour/ns) 46: Performance: 951.149 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (48 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 194.4 46: (ns/day) (hour/ns) 46: Performance: 399.857 0.060 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.9 46: (ns/day) (hour/ns) 46: Performance: 979.115 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (48 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 194.6 46: (ns/day) (hour/ns) 46: Performance: 460.192 0.052 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.6 46: (ns/day) (hour/ns) 46: Performance: 1067.694 0.022 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (47 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 193.5 46: (ns/day) (hour/ns) 46: Performance: 394.530 0.061 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.0 46: (ns/day) (hour/ns) 46: Performance: 1030.200 0.023 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (48 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 195.1 46: (ns/day) (hour/ns) 46: Performance: 386.729 0.062 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.3 46: (ns/day) (hour/ns) 46: Performance: 992.044 0.024 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (48 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.008 0.004 195.1 46: (ns/day) (hour/ns) 46: Performance: 367.797 0.065 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 23 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.5 46: (ns/day) (hour/ns) 46: Performance: 964.401 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (48 ms) 46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (1385 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 58 tests from 5 test cases ran. (6224 ms total) 46: [ PASSED ] 58 tests. 46/54 Test #46: MdrunNonIntegratorTests ............. Passed 6.25 sec test 47 Start 47: MdrunTpiTests 47: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunTpiTests.xml" 47: Test timeout computed to be: 600 47: [==========] Running 2 tests from 1 test case. 47: [----------] Global test environment set-up. 47: [----------] 2 tests from Simple/TpiTest 47: [ RUN ] Simple/TpiTest.ReproducesOutput/0 47: Ignoring obsolete mdp entry 'ns_type' 47: Generated 331705 of the 331705 non-bonded parameter combinations 47: Generating 1-4 interactions: fudge = 0.5 47: Generated 331705 of the 331705 1-4 parameter combinations 47: Excluding 2 bonded neighbours molecule type 'SOL' 47: Excluding 3 bonded neighbours molecule type 'methane' 47: Number of degrees of freedom in T-Coupling group System is 1308.00 47: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 47: log). 47: The current CPU can measure timings more accurately than the code in 47: mdrun-tpi-test was configured to use. This might affect your simulation 47: speed as accurate timings are needed for load-balancing. 47: Please consider rebuilding mdrun-tpi-test with the GMX_USE_RDTSCP=ON CMake option. 47: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 47: 47: TPI is not implemented for GPUs. 47: 47: Using 1 MPI thread 47: 47: Non-default thread affinity set, disabling internal thread affinity 47: 47: Using 1 OpenMP thread 47: 47: Reading frames from gro file '216 water molecules', 648 atoms. 47: Reading frame 0 time 0.000 mu 8.706e+02 8.706e+02 47: Last frame 0 time 0.000 47: Analysing residue names: 47: There are: 216 Water residues 47: There are: 1 Other residues 47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 47: This run will generate roughly 0 Mb of data 47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (792 ms) 47: [ RUN ] Simple/TpiTest.ReproducesOutput/1 47: Ignoring obsolete mdp entry 'ns_type' 47: Generated 331705 of the 331705 non-bonded parameter combinations 47: Generating 1-4 interactions: fudge = 0.5 47: Generated 331705 of the 331705 1-4 parameter combinations 47: Excluding 2 bonded neighbours molecule type 'SOL' 47: Excluding 3 bonded neighbours molecule type 'methane' 47: Number of degrees of freedom in T-Coupling group System is 1308.00 47: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 47: log). 47: The current CPU can measure timings more accurately than the code in 47: mdrun-tpi-test was configured to use. This might affect your simulation 47: speed as accurate timings are needed for load-balancing. 47: Please consider rebuilding mdrun-tpi-test with the GMX_USE_RDTSCP=ON CMake option. 47: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 47: 47: TPI is not implemented for GPUs. 47: 47: Using 1 MPI thread 47: 47: Non-default thread affinity set, disabling internal thread affinity 47: 47: Using 1 OpenMP thread 47: 47: Reading frames from gro file '216 water molecules', 648 atoms. 47: Reading frame 0 time 0.000 mu 9.144e+01 9.144e+01 47: Last frame 0 time 0.000 47: Analysing residue names: 47: There are: 216 Water residues 47: There are: 1 Other residues 47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 47: This run will generate roughly 0 Mb of data 47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (645 ms) 47: [----------] 2 tests from Simple/TpiTest (1437 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 2 tests from 1 test case ran. (1437 ms total) 47: [ PASSED ] 2 tests. 47/54 Test #47: MdrunTpiTests ....................... Passed 1.46 sec test 48 Start 48: MdrunMpiTests 48: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunMpiTests.xml" 48: Test timeout computed to be: 600 48: [==========] Running 22 tests from 7 test cases. 48: [----------] Global test environment set-up. 48: [----------] 1 test from DomainDecompositionSpecialCasesTest 48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to 515272695 48: Generated 3 of the 3 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 3 of the 3 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 9.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc2' 48: 0 steps, 0.0 ps. 48: 48: NOTE: 24 % of the run time was spent in domain decomposition, 48: 17 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.001 0.000 312.4 48: (ns/day) (hour/ns) 48: Performance: 226.351 0.106 48: This run will generate roughly 0 Mb of data 48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (255 ms) 48: [----------] 1 test from DomainDecompositionSpecialCasesTest (256 ms total) 48: 48: [----------] 4 tests from MimicTest 48: [ RUN ] MimicTest.OneQuantumMol 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -42156033 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 67 % of the run time was spent in domain decomposition, 48: 10 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.249 0.062 399.7 48: (ns/day) (hour/ns) 48: Performance: 1.388 17.293 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.OneQuantumMol (175 ms) 48: [ RUN ] MimicTest.AllQuantumMol 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to 1870659313 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 70 % of the run time was spent in domain decomposition, 48: 14 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.593 0.148 399.9 48: (ns/day) (hour/ns) 48: Performance: 0.583 41.181 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.AllQuantumMol (340 ms) 48: [ RUN ] MimicTest.TwoQuantumMol 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to 2144550847 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 90 % of the run time was spent in domain decomposition, 48: 0 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.177 0.044 399.6 48: (ns/day) (hour/ns) 48: Performance: 1.951 12.303 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.TwoQuantumMol (220 ms) 48: [ RUN ] MimicTest.BondCuts 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -814743589 48: Generated 2211 of the 2211 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2211 of the 2211 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 48: Number of degrees of freedom in T-Coupling group rest is 66.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: NVE simulation: will use the initial temperature of 300.368 K for 48: determining the Verlet buffer size 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/ala.gro' 48: 48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 70 % of the run time was spent in domain decomposition, 48: 0 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.194 0.048 399.7 48: (ns/day) (hour/ns) 48: Performance: 1.784 13.453 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.BondCuts (172 ms) 48: [----------] 4 tests from MimicTest (907 ms total) 48: 48: [----------] 1 test from MultiSimTerminationTest 48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 48: [----------] 1 test from MultiSimTerminationTest (0 ms total) 48: 48: [----------] 3 tests from PmeTest 48: [ RUN ] PmeTest.ReproducesEnergies 48: Setting the LD random seed to -545325318 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 12.00 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 48: NVE simulation: will use the initial temperature of 1046.791 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 48: This run will generate roughly 0 Mb of data 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.885 0.221 399.9 48: (ns/day) (hour/ns) 48: Performance: 8.197 2.928 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.459 0.115 399.6 48: (ns/day) (hour/ns) 48: Performance: 15.797 1.519 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.150 0.039 384.5 48: (ns/day) (hour/ns) 48: Performance: 46.402 0.517 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (1003 ms) 48: [ RUN ] PmeTest.ScalesTheBox 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -25464937 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 12.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: NVE simulation: will use the initial temperature of 1046.791 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 0 steps, 0.0 ps. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.003 0.001 362.6 48: (ns/day) (hour/ns) 48: Performance: 113.370 0.212 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 48: This run will generate roughly 0 Mb of data 48: [ OK ] PmeTest.ScalesTheBox (57 ms) 48: [ RUN ] PmeTest.ScalesTheBoxWithWalls 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -576193539 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Searching the wall atom type(s) 48: Number of degrees of freedom in T-Coupling group rest is 13.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: NVE simulation: will use the initial temperature of 966.268 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 0 steps, 0.0 ps. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.064 0.016 394.9 48: (ns/day) (hour/ns) 48: Performance: 5.314 4.517 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 48: This run will generate roughly 0 Mb of data 48: [ OK ] PmeTest.ScalesTheBoxWithWalls (709 ms) 48: [----------] 3 tests from PmeTest (1769 ms total) 48: 48: [----------] 1 test from ReplicaExchangeTerminationTest 48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 48: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total) 48: 48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 330891 of the 330891 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 330891 of the 330891 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -4.7991085e+01 48: Maximum force = 1.8629604e+02 on atom 13 48: Norm of force = 8.7722017e+01 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (720 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 330891 of the 330891 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 330891 of the 330891 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 3.02331e+02 on atom 3 48: F-Norm = 1.18024e+02 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -5.5862099e+01 48: Maximum force = 4.2728506e+02 on atom 13 48: Norm of force = 1.8453371e+02 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (660 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 22.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 3.1937704e+02 48: Maximum force = 9.9988633e+03 on atom 9 48: Norm of force = 4.6166993e+03 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (223 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: 48: NOTE 3 [file glycine_vacuo.top, line 12]: 48: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 48: 48: Number of degrees of freedom in T-Coupling group System is 22.00 48: 48: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 4 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 2.41575e+04 on atom 10 48: F-Norm = 1.18451e+04 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 1.5174426e+02 48: Maximum force = 7.4208862e+03 on atom 9 48: Norm of force = 3.5692992e+03 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (279 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 2145 of the 2145 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2145 of the 2145 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 48: 48: NOTE 3 [file unknown]: 48: You are using constraints on all bonds, whereas the forcefield has been 48: parametrized only with constraints involving hydrogen atoms. We suggest 48: using constraints = h-bonds instead, this will also improve performance. 48: 48: Cleaning up constraints and constant bonded interactions with virtual sites 48: Removed 18 Angles with virtual sites, 21 left 48: Removed 10 Proper Dih.s with virtual sites, 44 left 48: Converted 15 Constraints with virtual sites to connections, 7 left 48: Number of degrees of freedom in T-Coupling group System is 23.00 48: 48: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 4 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -1.5698444e+02 48: Maximum force = 4.5699698e+02 on atom 17 48: Norm of force = 1.8326839e+02 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (187 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 2145 of the 2145 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2145 of the 2145 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 48: 48: NOTE 3 [file unknown]: 48: You are using constraints on all bonds, whereas the forcefield has been 48: parametrized only with constraints involving hydrogen atoms. We suggest 48: using constraints = h-bonds instead, this will also improve performance. 48: 48: 48: NOTE 4 [file unknown]: 48: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 48: 48: Cleaning up constraints and constant bonded interactions with virtual sites 48: Removed 18 Angles with virtual sites, 21 left 48: Removed 10 Proper Dih.s with virtual sites, 44 left 48: Converted 15 Constraints with virtual sites to connections, 7 left 48: Number of degrees of freedom in T-Coupling group System is 23.00 48: 48: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 5 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 1.06802e+03 on atom 28 48: F-Norm = 4.26922e+02 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -1.6941107e+02 48: Maximum force = 2.1829741e+02 on atom 17 48: Norm of force = 7.9203227e+01 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (2514 ms) 48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4583 ms total) 48: 48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents converged to Fmax < 10 in 1 steps 48: Potential Energy = -9.7425687e-01 48: Maximum force = 4.0132279e+00 on atom 3 48: Norm of force = 1.6383933e+00 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (64 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 4.01323e+00 on atom 3 48: F-Norm = 1.63839e+00 48: 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 48: Potential Energy = -9.9064195e-01 48: Maximum force = 2.5781672e+00 on atom 3 48: Norm of force = 1.0525324e+00 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (184 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: 48: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: 48: There was 1 warning 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (4 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 3.1939685e+02 48: Maximum force = 9.9704248e+03 on atom 9 48: Norm of force = 4.6227568e+03 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (644 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 2.41672e+04 on atom 10 48: F-Norm = 1.19357e+04 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 1.5625761e+02 48: Maximum force = 7.5018237e+03 on atom 9 48: Norm of force = 3.6139019e+03 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (378 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: 48: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: 48: There was 1 warning 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (150 ms) 48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1424 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 22 tests from 7 test cases ran. (8939 ms total) 48: [ PASSED ] 22 tests. 48: 48: YOU HAVE 4 DISABLED TESTS 48: 48/54 Test #48: MdrunMpiTests ....................... Passed 8.96 sec test 49 Start 49: MdrunMpiCoordinationTestsOneRank 49: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml" 49: Test timeout computed to be: 960 49: [==========] Running 27 tests from 3 test cases. 49: [----------] Global test environment set-up. 49: [----------] 1 test from BasicPropagators/PeriodicActionsTest 49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 543.646 0.044 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1323.152 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1469.958 0.016 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.6 49: (ns/day) (hour/ns) 49: Performance: 1288.019 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1357.557 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1300.801 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (189 ms) 49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (189 ms total) 49: 49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.5 49: (ns/day) (hour/ns) 49: Performance: 1104.841 0.022 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1433.029 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1425.733 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1436.706 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.2 49: (ns/day) (hour/ns) 49: Performance: 646.510 0.037 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1464.716 0.016 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (45 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1350.711 0.018 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1277.072 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1365.077 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1339.260 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1334.617 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.5 49: (ns/day) (hour/ns) 49: Performance: 1077.215 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (43 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.4 49: (ns/day) (hour/ns) 49: Performance: 1463.672 0.016 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1308.259 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1412.332 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1375.747 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1351.897 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 573.399 0.042 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (46 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.2 49: (ns/day) (hour/ns) 49: Performance: 594.709 0.040 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 97.9 49: (ns/day) (hour/ns) 49: Performance: 607.075 0.040 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.2 49: (ns/day) (hour/ns) 49: Performance: 566.023 0.042 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.8 49: (ns/day) (hour/ns) 49: Performance: 902.122 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.7 49: (ns/day) (hour/ns) 49: Performance: 852.559 0.028 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1366.591 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (49 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.3 49: (ns/day) (hour/ns) 49: Performance: 814.247 0.029 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.6 49: (ns/day) (hour/ns) 49: Performance: 994.928 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.8 49: (ns/day) (hour/ns) 49: Performance: 806.889 0.030 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.5 49: (ns/day) (hour/ns) 49: Performance: 975.858 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.5 49: (ns/day) (hour/ns) 49: Performance: 1027.108 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1230.642 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (54 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 97.5 49: (ns/day) (hour/ns) 49: Performance: 742.598 0.032 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.2 49: (ns/day) (hour/ns) 49: Performance: 1369.325 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1389.399 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1428.047 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1320.033 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1332.885 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (44 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 97.8 49: (ns/day) (hour/ns) 49: Performance: 728.719 0.033 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1432.696 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1323.720 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1287.211 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1363.868 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 97.5 49: (ns/day) (hour/ns) 49: Performance: 741.169 0.032 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (44 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 97.7 49: (ns/day) (hour/ns) 49: Performance: 692.357 0.035 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1430.700 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1455.373 0.016 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1441.749 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1419.492 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.4 49: (ns/day) (hour/ns) 49: Performance: 1487.707 0.016 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (44 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.4 49: (ns/day) (hour/ns) 49: Performance: 1478.070 0.016 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.0 49: (ns/day) (hour/ns) 49: Performance: 1262.158 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.4 49: (ns/day) (hour/ns) 49: Performance: 1301.351 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1448.188 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.4 49: (ns/day) (hour/ns) 49: Performance: 1471.362 0.016 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.3 49: (ns/day) (hour/ns) 49: Performance: 1504.418 0.016 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (40 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1502.950 0.016 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1412.332 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1447.848 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1393.799 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1480.912 0.016 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1399.817 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (36 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1436.036 0.017 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1488.785 0.016 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1209.382 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1317.774 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1374.826 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1392.225 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (38 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1467.157 0.016 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1309.372 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1394.430 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1468.906 0.016 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1240.055 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1440.738 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (37 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 97.5 49: (ns/day) (hour/ns) 49: Performance: 1302.451 0.018 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.7 49: (ns/day) (hour/ns) 49: Performance: 1249.867 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.7 49: (ns/day) (hour/ns) 49: Performance: 1135.175 0.021 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.6 49: (ns/day) (hour/ns) 49: Performance: 1286.674 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.6 49: (ns/day) (hour/ns) 49: Performance: 1223.311 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.8 49: (ns/day) (hour/ns) 49: Performance: 1234.588 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (37 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1173.000 0.020 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1348.937 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 84.8 49: (ns/day) (hour/ns) 49: Performance: 1184.274 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1385.960 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1101.089 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1332.308 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (37 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.4 49: (ns/day) (hour/ns) 49: Performance: 1272.587 0.019 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.8 49: (ns/day) (hour/ns) 49: Performance: 1058.885 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.6 49: (ns/day) (hour/ns) 49: Performance: 1269.702 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.8 49: (ns/day) (hour/ns) 49: Performance: 1124.812 0.021 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.5 49: (ns/day) (hour/ns) 49: Performance: 1305.487 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.8 49: (ns/day) (hour/ns) 49: Performance: 1221.613 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (39 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1434.364 0.017 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1196.000 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1231.134 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1392.225 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1307.149 0.018 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1387.521 0.017 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (38 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.3 49: (ns/day) (hour/ns) 49: Performance: 1171.661 0.020 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.5 49: (ns/day) (hour/ns) 49: Performance: 1199.493 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.6 49: (ns/day) (hour/ns) 49: Performance: 1225.989 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.6 49: (ns/day) (hour/ns) 49: Performance: 1170.770 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.8 49: (ns/day) (hour/ns) 49: Performance: 1109.018 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.5 49: (ns/day) (hour/ns) 49: Performance: 1233.352 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (37 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.7 49: (ns/day) (hour/ns) 49: Performance: 1090.371 0.022 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.7 49: (ns/day) (hour/ns) 49: Performance: 1071.408 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 97.1 49: (ns/day) (hour/ns) 49: Performance: 910.522 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.8 49: (ns/day) (hour/ns) 49: Performance: 1034.698 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.5 49: (ns/day) (hour/ns) 49: Performance: 965.308 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.6 49: (ns/day) (hour/ns) 49: Performance: 1071.221 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (40 ms) 49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (748 ms total) 49: 49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.009 0.009 99.3 49: (ns/day) (hour/ns) 49: Performance: 157.681 0.152 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.9 49: (ns/day) (hour/ns) 49: Performance: 529.670 0.045 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1156.051 0.021 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.9 49: (ns/day) (hour/ns) 49: Performance: 276.595 0.087 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.1 49: (ns/day) (hour/ns) 49: Performance: 1234.835 0.019 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1016.097 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (4400 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1019.291 0.024 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 95.7 49: (ns/day) (hour/ns) 49: Performance: 897.392 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.2 49: (ns/day) (hour/ns) 49: Performance: 440.987 0.054 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.3 49: (ns/day) (hour/ns) 49: Performance: 1037.137 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1061.439 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1117.264 0.021 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (3031 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1127.282 0.021 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1213.432 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1221.613 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.9 49: (ns/day) (hour/ns) 49: Performance: 767.962 0.031 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 507.504 0.047 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1209.620 0.020 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (2984 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1168.328 0.021 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1066.400 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1166.337 0.021 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1088.636 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1169.881 0.021 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1073.274 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3391 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1213.193 0.020 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1150.867 0.021 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1041.697 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.5 49: (ns/day) (hour/ns) 49: Performance: 1057.794 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.2 49: (ns/day) (hour/ns) 49: Performance: 518.438 0.046 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.0 49: (ns/day) (hour/ns) 49: Performance: 519.837 0.046 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2948 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.7 49: (ns/day) (hour/ns) 49: Performance: 523.994 0.046 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1117.467 0.021 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1014.758 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.9 49: (ns/day) (hour/ns) 49: Performance: 270.914 0.089 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.0 49: (ns/day) (hour/ns) 49: Performance: 530.994 0.045 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1084.803 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4089 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.3 49: (ns/day) (hour/ns) 49: Performance: 526.501 0.046 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.5 49: (ns/day) (hour/ns) 49: Performance: 1001.234 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.7 49: (ns/day) (hour/ns) 49: Performance: 919.492 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.3 49: (ns/day) (hour/ns) 49: Performance: 460.124 0.052 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.3 49: (ns/day) (hour/ns) 49: Performance: 463.970 0.052 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.6 49: (ns/day) (hour/ns) 49: Performance: 1019.291 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2860 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.6 49: (ns/day) (hour/ns) 49: Performance: 982.864 0.024 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.6 49: (ns/day) (hour/ns) 49: Performance: 893.099 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.7 49: (ns/day) (hour/ns) 49: Performance: 901.199 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.1 49: (ns/day) (hour/ns) 49: Performance: 470.023 0.051 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 98.5 49: (ns/day) (hour/ns) 49: Performance: 972.009 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.7 49: (ns/day) (hour/ns) 49: Performance: 895.305 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3044 ms) 49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (26747 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 27 tests from 3 test cases ran. (27684 ms total) 49: [ PASSED ] 27 tests. 49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 27.70 sec test 50 Start 50: MdrunMpiCoordinationTestsTwoRanks 50: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml" 50: Test timeout computed to be: 960 50: [==========] Running 27 tests from 3 test cases. 50: [----------] Global test environment set-up. 50: [----------] 1 test from BasicPropagators/PeriodicActionsTest 50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.9%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 195.9 50: (ns/day) (hour/ns) 50: Performance: 482.125 0.050 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 36.7%. 50: The balanceable part of the MD step is 32%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 11.7%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: NOTE: 11.7 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You can consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 20 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 16 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 1.184 0.608 194.7 50: (ns/day) (hour/ns) 50: Performance: 2.416 9.934 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 39.6%. 50: The balanceable part of the MD step is 36%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 14.3%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: NOTE: 14.3 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You can consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 18 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 17 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 1.776 0.926 191.8 50: (ns/day) (hour/ns) 50: Performance: 1.586 15.129 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.6%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.8%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.2 50: (ns/day) (hour/ns) 50: Performance: 1044.257 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 38.4%. 50: The balanceable part of the MD step is 34%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 13.1%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: NOTE: 13.1 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You can consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 18 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 16 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.156 1.114 193.5 50: (ns/day) (hour/ns) 50: Performance: 1.319 18.202 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.5%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.3 50: (ns/day) (hour/ns) 50: Performance: 1008.115 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (6290 ms) 50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (6290 ms total) 50: 50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.8%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.2 50: (ns/day) (hour/ns) 50: Performance: 1069.733 0.022 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.3%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.6%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 192.0 50: (ns/day) (hour/ns) 50: Performance: 991.725 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.8%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.4 50: (ns/day) (hour/ns) 50: Performance: 994.607 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.3%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 969.790 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.1%. 50: The balanceable part of the MD step is 46%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.4 50: (ns/day) (hour/ns) 50: Performance: 992.444 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.5%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.0 50: (ns/day) (hour/ns) 50: Performance: 1030.975 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1168 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.2%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.1%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.4 50: (ns/day) (hour/ns) 50: Performance: 1031.666 0.023 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.9%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.4%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.7 50: (ns/day) (hour/ns) 50: Performance: 993.965 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.2%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.1%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.2 50: (ns/day) (hour/ns) 50: Performance: 1049.416 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 7.6%. 50: The balanceable part of the MD step is 1%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.1%. 50: 50: 50: NOTE: 68 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 12 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.102 0.051 199.7 50: (ns/day) (hour/ns) 50: Performance: 28.704 0.836 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.1%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.3 50: (ns/day) (hour/ns) 50: Performance: 1014.841 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.8%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 952.767 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (748 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 38.6%. 50: The balanceable part of the MD step is 34%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 13.1%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: NOTE: 13.1 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You can consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 19 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 16 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.236 1.154 193.8 50: (ns/day) (hour/ns) 50: Performance: 1.273 18.856 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.5%. 50: The balanceable part of the MD step is 46%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.7%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.8 50: (ns/day) (hour/ns) 50: Performance: 982.238 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.8%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.4%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.6 50: (ns/day) (hour/ns) 50: Performance: 989.495 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.3%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.7%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 189.7 50: (ns/day) (hour/ns) 50: Performance: 1007.703 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.3%. 50: The balanceable part of the MD step is 46%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.6%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.9 50: (ns/day) (hour/ns) 50: Performance: 942.708 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.5%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.5 50: (ns/day) (hour/ns) 50: Performance: 997.586 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3084 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.5 50: (ns/day) (hour/ns) 50: Performance: 1097.363 0.022 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 928.220 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.6 50: (ns/day) (hour/ns) 50: Performance: 1104.346 0.022 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.7 50: (ns/day) (hour/ns) 50: Performance: 953.062 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.1 50: (ns/day) (hour/ns) 50: Performance: 971.626 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.5 50: (ns/day) (hour/ns) 50: Performance: 1071.967 0.022 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (468 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.067 0.034 199.5 50: (ns/day) (hour/ns) 50: Performance: 43.820 0.548 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.3 50: (ns/day) (hour/ns) 50: Performance: 892.581 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 33 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.002 0.001 190.8 50: (ns/day) (hour/ns) 50: Performance: 1140.428 0.021 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.002 0.001 190.6 50: (ns/day) (hour/ns) 50: Performance: 1147.224 0.021 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 33 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.002 0.001 190.7 50: (ns/day) (hour/ns) 50: Performance: 1128.727 0.021 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 189.2 50: (ns/day) (hour/ns) 50: Performance: 1089.792 0.022 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (572 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 189.3 50: (ns/day) (hour/ns) 50: Performance: 1013.006 0.024 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 189.8 50: (ns/day) (hour/ns) 50: Performance: 1072.527 0.022 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.002 0.001 190.6 50: (ns/day) (hour/ns) 50: Performance: 1154.101 0.021 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 33 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.7 50: (ns/day) (hour/ns) 50: Performance: 1105.535 0.022 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.1 50: (ns/day) (hour/ns) 50: Performance: 1071.314 0.022 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.002 0.001 190.7 50: (ns/day) (hour/ns) 50: Performance: 1122.353 0.021 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (772 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 33 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.002 0.001 191.0 50: (ns/day) (hour/ns) 50: Performance: 1172.330 0.020 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.5 50: (ns/day) (hour/ns) 50: Performance: 1085.376 0.022 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 33 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.4 50: (ns/day) (hour/ns) 50: Performance: 1080.332 0.022 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 21 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 1.708 0.886 192.8 50: (ns/day) (hour/ns) 50: Performance: 1.658 14.477 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.139 0.070 199.8 50: (ns/day) (hour/ns) 50: Performance: 21.114 1.137 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.4 50: (ns/day) (hour/ns) 50: Performance: 1081.280 0.022 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2884 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.0 50: (ns/day) (hour/ns) 50: Performance: 1066.216 0.023 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 189.9 50: (ns/day) (hour/ns) 50: Performance: 1037.224 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.0 50: (ns/day) (hour/ns) 50: Performance: 1043.903 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 964.477 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 189.7 50: (ns/day) (hour/ns) 50: Performance: 1044.877 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 189.1 50: (ns/day) (hour/ns) 50: Performance: 1048.701 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1064 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 189.5 50: (ns/day) (hour/ns) 50: Performance: 971.932 0.025 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 189.8 50: (ns/day) (hour/ns) 50: Performance: 950.122 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.2 50: (ns/day) (hour/ns) 50: Performance: 1026.680 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.0 50: (ns/day) (hour/ns) 50: Performance: 992.923 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.5 50: (ns/day) (hour/ns) 50: Performance: 988.383 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 189.8 50: (ns/day) (hour/ns) 50: Performance: 1056.162 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (912 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 13 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 19 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 1.078 0.539 200.0 50: (ns/day) (hour/ns) 50: Performance: 2.724 8.811 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.5 50: (ns/day) (hour/ns) 50: Performance: 1005.811 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.1 50: (ns/day) (hour/ns) 50: Performance: 979.582 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 876.204 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.4 50: (ns/day) (hour/ns) 50: Performance: 1031.407 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.2 50: (ns/day) (hour/ns) 50: Performance: 896.673 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2636 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.4 50: (ns/day) (hour/ns) 50: Performance: 1028.222 0.023 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.5 50: (ns/day) (hour/ns) 50: Performance: 1056.343 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.6 50: (ns/day) (hour/ns) 50: Performance: 972.009 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.8 50: (ns/day) (hour/ns) 50: Performance: 1022.590 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.8 50: (ns/day) (hour/ns) 50: Performance: 1030.200 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.1 50: (ns/day) (hour/ns) 50: Performance: 906.303 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (608 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.8 50: (ns/day) (hour/ns) 50: Performance: 1000.340 0.024 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.3 50: (ns/day) (hour/ns) 50: Performance: 994.767 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.6 50: (ns/day) (hour/ns) 50: Performance: 1009.851 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.4 50: (ns/day) (hour/ns) 50: Performance: 960.267 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.7 50: (ns/day) (hour/ns) 50: Performance: 1030.889 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.6 50: (ns/day) (hour/ns) 50: Performance: 1036.875 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1160 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.9%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.7%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.1 50: (ns/day) (hour/ns) 50: Performance: 772.198 0.031 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.7%. 50: The balanceable part of the MD step is 57%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.5 50: (ns/day) (hour/ns) 50: Performance: 762.214 0.031 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.7%. 50: The balanceable part of the MD step is 61%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 72 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.064 0.032 199.4 50: (ns/day) (hour/ns) 50: Performance: 46.035 0.521 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.6%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.9 50: (ns/day) (hour/ns) 50: Performance: 733.273 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 4.0%. 50: The balanceable part of the MD step is 54%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.2%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 735.374 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.5%. 50: The balanceable part of the MD step is 59%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 832.232 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (832 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.7%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 890.452 0.027 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.0%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.5%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.4 50: (ns/day) (hour/ns) 50: Performance: 897.784 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.2%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 825.153 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.2%. 50: The balanceable part of the MD step is 52%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.6%. 50: 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.4 50: (ns/day) (hour/ns) 50: Performance: 885.397 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 31.9%. 50: The balanceable part of the MD step is 24%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 7.6%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You can consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 56 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.108 0.054 199.7 50: (ns/day) (hour/ns) 50: Performance: 27.196 0.882 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.7%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.4 50: (ns/day) (hour/ns) 50: Performance: 901.726 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1740 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.5 50: (ns/day) (hour/ns) 50: Performance: 819.827 0.029 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 23 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 3.032 1.554 195.1 50: (ns/day) (hour/ns) 50: Performance: 0.945 25.392 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 23 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.968 1.534 193.5 50: (ns/day) (hour/ns) 50: Performance: 0.958 25.065 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.020 20.8 50: (ns/day) (hour/ns) 50: Performance: 74.528 0.322 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.2 50: (ns/day) (hour/ns) 50: Performance: 895.565 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.6 50: (ns/day) (hour/ns) 50: Performance: 825.596 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (5412 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.6 50: (ns/day) (hour/ns) 50: Performance: 1015.929 0.024 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 33 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.5 50: (ns/day) (hour/ns) 50: Performance: 982.864 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.2 50: (ns/day) (hour/ns) 50: Performance: 1051.296 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.3 50: (ns/day) (hour/ns) 50: Performance: 1023.865 0.023 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.512 1.292 194.4 50: (ns/day) (hour/ns) 50: Performance: 1.137 21.110 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 33 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.7 50: (ns/day) (hour/ns) 50: Performance: 977.950 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (3384 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.3 50: (ns/day) (hour/ns) 50: Performance: 883.366 0.027 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.6 50: (ns/day) (hour/ns) 50: Performance: 932.646 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.4 50: (ns/day) (hour/ns) 50: Performance: 889.295 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.4 50: (ns/day) (hour/ns) 50: Performance: 819.173 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.2 50: (ns/day) (hour/ns) 50: Performance: 901.001 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.7 50: (ns/day) (hour/ns) 50: Performance: 953.800 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (900 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 26 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.7 50: (ns/day) (hour/ns) 50: Performance: 764.911 0.031 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 50 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.532 1.298 195.1 50: (ns/day) (hour/ns) 50: Performance: 1.132 21.208 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 50 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.328 1.182 197.0 50: (ns/day) (hour/ns) 50: Performance: 1.243 19.312 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 27 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.1 50: (ns/day) (hour/ns) 50: Performance: 738.946 0.032 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 738.370 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 27 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 193.0 50: (ns/day) (hour/ns) 50: Performance: 732.532 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (6064 ms) 50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (34408 ms total) 50: 50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 8.2%. 50: The balanceable part of the MD step is 33%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.7%. 50: 50: 50: NOTE: 16 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 13 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.672 1.364 195.9 50: (ns/day) (hour/ns) 50: Performance: 1.077 22.287 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 4.8%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.3%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 189.5 50: (ns/day) (hour/ns) 50: Performance: 807.841 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 4.1%. 50: The balanceable part of the MD step is 34%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.4%. 50: 50: 50: NOTE: 17 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 13 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 3.008 1.540 195.3 50: (ns/day) (hour/ns) 50: Performance: 0.954 25.160 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.6%. 50: The balanceable part of the MD step is 55%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.4%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 192.6 50: (ns/day) (hour/ns) 50: Performance: 986.247 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 4.1%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.0%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.1 50: (ns/day) (hour/ns) 50: Performance: 869.833 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 6.6%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.2%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 829.598 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (18116 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 9.9%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 4.8%. 50: 50: 50: NOTE: 27 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.4 50: (ns/day) (hour/ns) 50: Performance: 758.274 0.032 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 5.4%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.6%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.5 50: (ns/day) (hour/ns) 50: Performance: 791.342 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 6.4%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.0%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 791.037 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 5.5%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.6%. 50: 50: 50: NOTE: 27 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.4 50: (ns/day) (hour/ns) 50: Performance: 841.611 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 7.8%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.7%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 805.306 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 4.6%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.3%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.9 50: (ns/day) (hour/ns) 50: Performance: 809.965 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (14529 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 893.487 0.027 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 780.464 0.031 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 189.9 50: (ns/day) (hour/ns) 50: Performance: 731.749 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 835.901 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 815.703 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.6 50: (ns/day) (hour/ns) 50: Performance: 717.600 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (14396 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 901.462 0.027 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.1 50: (ns/day) (hour/ns) 50: Performance: 880.273 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.178 0.089 199.7 50: (ns/day) (hour/ns) 50: Performance: 16.463 1.458 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.6 50: (ns/day) (hour/ns) 50: Performance: 808.318 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.3 50: (ns/day) (hour/ns) 50: Performance: 879.959 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 7 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.6 50: (ns/day) (hour/ns) 50: Performance: 820.537 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (14712 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 193.1 50: (ns/day) (hour/ns) 50: Performance: 769.978 0.031 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.6 50: (ns/day) (hour/ns) 50: Performance: 832.232 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.3 50: (ns/day) (hour/ns) 50: Performance: 754.882 0.032 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.4 50: (ns/day) (hour/ns) 50: Performance: 714.852 0.034 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.5 50: (ns/day) (hour/ns) 50: Performance: 834.882 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.8 50: (ns/day) (hour/ns) 50: Performance: 804.780 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (13559 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 815.487 0.029 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 700.585 0.034 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.1 50: (ns/day) (hour/ns) 50: Performance: 847.166 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 193.0 50: (ns/day) (hour/ns) 50: Performance: 692.785 0.035 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 46 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.159 0.123 129.1 50: (ns/day) (hour/ns) 50: Performance: 11.933 2.011 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.021 0.034 62.1 50: (ns/day) (hour/ns) 50: Performance: 43.820 0.548 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (15276 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 5.8%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.4%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.3 50: (ns/day) (hour/ns) 50: Performance: 687.912 0.035 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 4.6%. 50: The balanceable part of the MD step is 54%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.5%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.7 50: (ns/day) (hour/ns) 50: Performance: 659.240 0.036 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 5.9%. 50: The balanceable part of the MD step is 57%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.3%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.5 50: (ns/day) (hour/ns) 50: Performance: 685.729 0.035 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 7.1%. 50: The balanceable part of the MD step is 60%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 4.3%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 659.063 0.036 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.1%. 50: The balanceable part of the MD step is 57%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 190.0 50: (ns/day) (hour/ns) 50: Performance: 599.951 0.040 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.6%. 50: The balanceable part of the MD step is 40%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 11 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 18 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 4.341 2.228 194.9 50: (ns/day) (hour/ns) 50: Performance: 0.659 36.405 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (17228 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 190.9 50: (ns/day) (hour/ns) 50: Performance: 591.001 0.041 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.003 191.6 50: (ns/day) (hour/ns) 50: Performance: 557.167 0.043 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 7 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.003 190.2 50: (ns/day) (hour/ns) 50: Performance: 561.074 0.043 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.080 0.040 199.2 50: (ns/day) (hour/ns) 50: Performance: 36.561 0.656 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 645.088 0.037 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.003 191.2 50: (ns/day) (hour/ns) 50: Performance: 572.147 0.042 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (13536 ms) 50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (121352 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 27 tests from 3 test cases ran. (162050 ms total) 50: [ PASSED ] 27 tests. 50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 162.08 sec test 51 Start 51: GmxapiExternalInterfaceTests 51: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 51: Test timeout computed to be: 600 51: [==========] Running 9 tests from 2 test cases. 51: [----------] Global test environment set-up. 51: [----------] 8 tests from GmxApiTest 51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 51: Setting the LD random seed to -5411167 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.002 0.001 189.8 51: (ns/day) (hour/ns) 51: Performance: 406.308 0.059 51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1946 ms) 51: [ RUN ] GmxApiTest.SystemConstruction 51: Setting the LD random seed to -539029509 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: [ OK ] GmxApiTest.SystemConstruction (1805 ms) 51: [ RUN ] GmxApiTest.SaneVersionComparisons 51: [ OK ] GmxApiTest.SaneVersionComparisons (12 ms) 51: [ RUN ] GmxApiTest.VersionNamed0_1_Features 51: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 51: [ RUN ] GmxApiTest.RunnerBasicMD 51: Setting the LD random seed to -872420036 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.003 0.001 190.8 51: (ns/day) (hour/ns) 51: Performance: 362.783 0.066 51: [ OK ] GmxApiTest.RunnerBasicMD (1831 ms) 51: [ RUN ] GmxApiTest.RunnerReinitialize 51: Setting the LD random seed to -742533205 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: 51: Received the remote INT/TERM signal, stopping within 50 steps 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.004 0.002 193.1 51: (ns/day) (hour/ns) 51: Performance: 1647.297 0.015 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.188 0.094 199.8 51: (ns/day) (hour/ns) 51: Performance: 37.678 0.637 51: [ OK ] GmxApiTest.RunnerReinitialize (1918 ms) 51: [ RUN ] GmxApiTest.RunnerContinuedMD 51: Setting the LD random seed to -1210056713 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 10 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.003 0.001 191.3 51: (ns/day) (hour/ns) 51: Performance: 1319.383 0.018 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: 51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.003 0.002 193.1 51: (ns/day) (hour/ns) 51: Performance: 2093.755 0.011 51: [ OK ] GmxApiTest.RunnerContinuedMD (1860 ms) 51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 51: Setting the LD random seed to -1913147494 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 1, rlist from 1.041 to 1 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 1 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: NOTE: 14 % of the run time was spent in pair search, 51: you might want to increase nstlist (this has no effect on accuracy) 51: 51: Core t (s) Wall t (s) (%) 51: Time: 1.128 0.564 200.0 51: (ns/day) (hour/ns) 51: Performance: 0.598 40.112 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: 51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps 51: Changing nstlist from 10 to 1, rlist from 1.041 to 1 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: 51: NOTE: 24 % of the run time was spent in pair search, 51: you might want to increase nstlist (this has no effect on accuracy) 51: 51: Core t (s) Wall t (s) (%) 51: Time: 1.050 0.525 200.0 51: (ns/day) (hour/ns) 51: Performance: 0.643 37.329 51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (1868 ms) 51: [----------] 8 tests from GmxApiTest (11241 ms total) 51: 51: [----------] 1 test from GmxApiBasicTest 51: [ RUN ] GmxApiBasicTest.Status 51: [ OK ] GmxApiBasicTest.Status (0 ms) 51: [----------] 1 test from GmxApiBasicTest (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 2 test cases ran. (11241 ms total) 51: [ PASSED ] 9 tests. 51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 11.31 sec test 52 Start 52: GmxapiMpiTests 52: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/GmxapiMpiTests.xml" 52: Test timeout computed to be: 600 52: [==========] Running 9 tests from 2 test cases. 52: [----------] Global test environment set-up. 52: [----------] 8 tests from GmxApiTest 52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 52: Setting the LD random seed to -269300801 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.003 0.001 189.7 52: (ns/day) (hour/ns) 52: Performance: 368.320 0.065 52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1531 ms) 52: [ RUN ] GmxApiTest.SystemConstruction 52: Setting the LD random seed to -759062529 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: [ OK ] GmxApiTest.SystemConstruction (512 ms) 52: [ RUN ] GmxApiTest.SaneVersionComparisons 52: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 52: [ RUN ] GmxApiTest.VersionNamed0_1_Features 52: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 52: [ RUN ] GmxApiTest.RunnerBasicMD 52: Setting the LD random seed to -1111789569 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.002 0.001 190.3 52: (ns/day) (hour/ns) 52: Performance: 397.114 0.060 52: [ OK ] GmxApiTest.RunnerBasicMD (817 ms) 52: [ RUN ] GmxApiTest.RunnerReinitialize 52: Setting the LD random seed to -4198721 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: 52: Received the remote INT/TERM signal, stopping within 50 steps 52: 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.004 0.002 192.7 52: (ns/day) (hour/ns) 52: Performance: 1929.080 0.012 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.018 0.009 198.5 52: (ns/day) (hour/ns) 52: Performance: 391.930 0.061 52: [ OK ] GmxApiTest.RunnerReinitialize (597 ms) 52: [ RUN ] GmxApiTest.RunnerContinuedMD 52: Setting the LD random seed to -1242304654 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 10 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.003 0.001 191.4 52: (ns/day) (hour/ns) 52: Performance: 1265.758 0.019 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: 52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.003 0.002 193.2 52: (ns/day) (hour/ns) 52: Performance: 2113.103 0.011 52: [ OK ] GmxApiTest.RunnerContinuedMD (518 ms) 52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 52: Setting the LD random seed to -1082147267 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 1, rlist from 1.041 to 1 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 1 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.002 0.001 190.0 52: (ns/day) (hour/ns) 52: Performance: 286.264 0.084 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: 52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps 52: Changing nstlist from 10 to 1, rlist from 1.041 to 1 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.002 0.001 187.1 52: (ns/day) (hour/ns) 52: Performance: 387.936 0.062 52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (507 ms) 52: [----------] 8 tests from GmxApiTest (4482 ms total) 52: 52: [----------] 1 test from GmxApiBasicTest 52: [ RUN ] GmxApiBasicTest.Status 52: [ OK ] GmxApiBasicTest.Status (0 ms) 52: [----------] 1 test from GmxApiBasicTest (0 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 9 tests from 2 test cases ran. (4482 ms total) 52: [ PASSED ] 9 tests. 52/54 Test #52: GmxapiMpiTests ...................... Passed 4.52 sec test 53 Start 53: GmxapiInternalInterfaceTests 53: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 53: Test timeout computed to be: 600 53: [==========] Running 2 tests from 1 test case. 53: [----------] Global test environment set-up. 53: [----------] 2 tests from GmxApiTest 53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 53: Setting the LD random seed to -679500297 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: Generating 1-4 interactions: fudge = 0.5 53: Generated 331705 of the 331705 1-4 parameter combinations 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: NOTE 1 [file spc_and_methane.top, line 33]: 53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 53: the time step of 2.0e-03 ps. 53: Maybe you forgot to change the constraints mdp option. 53: 53: Number of degrees of freedom in T-Coupling group System is 18.00 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 2 notes 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: This run will generate roughly 0 Mb of data 53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (516 ms) 53: [ RUN ] GmxApiTest.CreateApiWorkflow 53: Setting the LD random seed to -1310769 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: Generating 1-4 interactions: fudge = 0.5 53: Generated 331705 of the 331705 1-4 parameter combinations 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: NOTE 1 [file spc_and_methane.top, line 33]: 53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 53: the time step of 2.0e-03 ps. 53: Maybe you forgot to change the constraints mdp option. 53: 53: Number of degrees of freedom in T-Coupling group System is 18.00 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 2 notes 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: This run will generate roughly 0 Mb of data 53: [ OK ] GmxApiTest.CreateApiWorkflow (506 ms) 53: [----------] 2 tests from GmxApiTest (1022 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 2 tests from 1 test case ran. (1022 ms total) 53: [ PASSED ] 2 tests. 53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 1.08 sec test 54 Start 54: GmxapiInternalsMpiTests 54: Test command: /build/reproducible-path/gromacs-2020.6/build/basic/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic/Testing/Temporary/GmxapiInternalsMpiTests.xml" 54: Test timeout computed to be: 600 54: [==========] Running 2 tests from 1 test case. 54: [----------] Global test environment set-up. 54: [----------] 2 tests from GmxApiTest 54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 54: Setting the LD random seed to -396361729 54: Generated 331705 of the 331705 non-bonded parameter combinations 54: Generating 1-4 interactions: fudge = 0.5 54: Generated 331705 of the 331705 1-4 parameter combinations 54: Excluding 2 bonded neighbours molecule type 'SOL' 54: Excluding 3 bonded neighbours molecule type 'methane' 54: 54: NOTE 1 [file spc_and_methane.top, line 33]: 54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 54: the time step of 2.0e-03 ps. 54: Maybe you forgot to change the constraints mdp option. 54: 54: Number of degrees of freedom in T-Coupling group System is 18.00 54: 54: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 54: You are using a plain Coulomb cut-off, which might produce artifacts. 54: You might want to consider using PME electrostatics. 54: 54: 54: 54: There were 2 notes 54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 54: Note that mdrun will redetermine rlist based on the actual pair-list setup 54: This run will generate roughly 0 Mb of data 54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (788 ms) 54: [ RUN ] GmxApiTest.CreateApiWorkflow 54: Setting the LD random seed to -7235 54: Generated 331705 of the 331705 non-bonded parameter combinations 54: Generating 1-4 interactions: fudge = 0.5 54: Generated 331705 of the 331705 1-4 parameter combinations 54: Excluding 2 bonded neighbours molecule type 'SOL' 54: Excluding 3 bonded neighbours molecule type 'methane' 54: 54: NOTE 1 [file spc_and_methane.top, line 33]: 54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 54: the time step of 2.0e-03 ps. 54: Maybe you forgot to change the constraints mdp option. 54: 54: Number of degrees of freedom in T-Coupling group System is 18.00 54: 54: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 54: You are using a plain Coulomb cut-off, which might produce artifacts. 54: You might want to consider using PME electrostatics. 54: 54: 54: 54: There were 2 notes 54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 54: Note that mdrun will redetermine rlist based on the actual pair-list setup 54: This run will generate roughly 0 Mb of data 54: [ OK ] GmxApiTest.CreateApiWorkflow (501 ms) 54: [----------] 2 tests from GmxApiTest (1289 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 2 tests from 1 test case ran. (1289 ms total) 54: [ PASSED ] 2 tests. 54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 1.32 sec 100% tests passed, 0 tests failed out of 54 Label Time Summary: GTest = 252.58 sec*proc (54 tests) IntegrationTest = 43.91 sec*proc (12 tests) MpiTest = 205.91 sec*proc (8 tests) SlowTest = 189.78 sec*proc (2 tests) UnitTest = 18.89 sec*proc (40 tests) Total Test time (real) = 252.66 sec /usr/bin/make -j16 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles 85 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 0%] Built target lmfit_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 1%] Built target scanner /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend [ 1%] Built target release-version-info make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= [ 3%] Built target thread_mpi /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= [ 4%] Built target tng_io_obj make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/gtest /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build Scanning dependencies of target gtest /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 4%] Built target linearalgebra [ 5%] Built target modularsimulator /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 5%] Built target vmddlopen /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend [ 5%] Built target mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 67%] Built target libgromacs /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 68%] Built target gmxapi cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 68%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= Scanning dependencies of target gmock make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 68%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/testutils /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include 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/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/tinyxml2/tinyxml2.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 69%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend Scanning dependencies of target mdrun_test_infrastructure make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/energyreader.cpp Scanning dependencies of target testutils-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.cpp Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/mpitest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/mdmodulenotification.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/interactivetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/terminationhelper.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/refdata_tests.cpp Scanning dependencies of target mdlib-test make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build Scanning dependencies of target applied_forces-test make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/calc_verletbuf.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/mock_helptopic.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' Scanning dependencies of target domdec-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' Scanning dependencies of target utility-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfitting.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests/hashedmap.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/alignedallocator.cpp Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmebsplinetest.cpp /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fft/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/trajectorycomparison.cpp [ 69%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/trajectoryreader.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 69%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 69%] Built target onlinehelp-test-shared cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 69%] Built target fft-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 69%] Built target domdec-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmesplinespreadtest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 69%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdspan-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 70%] Built target hardware-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpformat.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 71%] Built target testutils-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 71%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= Scanning dependencies of target pbcutil-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests/pbc.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask128.cpp [ 72%] Built target applied_forces-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpwritercontext.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settletestdata.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 72%] Built target pbcutil-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 72%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/tables/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 72%] Built target restraintpotential-test Scanning dependencies of target table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tables/tests/splinetable.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/normaldistribution.cpp /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= Scanning dependencies of target topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/mutex.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 74%] Built target mdlib-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/symtab.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 74%] Built target ewald-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 74%] Built target taskassignment-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 74%] Built target pull-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/threefry.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 74%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/optional.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 75%] Built target topology-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxana-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/uniformrealdistribution.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx3-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp Scanning dependencies of target pdb2gmx2-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/multidimarray.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 75%] Built target table-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx1-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 75%] Built target mdspan-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_msd.cpp Scanning dependencies of target gmxpreprocess-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/grid.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 76%] Built target random-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= Scanning dependencies of target correlations-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/string_view.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 77%] Built target gmxana-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 77%] Built target awh-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color= Scanning dependencies of target coordinateio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 77%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target energyanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 78%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/tools/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= Scanning dependencies of target tool-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tools/tests/report_methods.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 78%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 80%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= Scanning dependencies of target selection-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/requirements.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 82%] Built target utility-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-modules-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 82%] Built target correlations-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-tpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tools/tests/trjconv.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_floatingpoint.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/interactiveMD.cpp [ 83%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_math.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-output-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/nbsearch.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-non-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 83%] Built target compat-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 83%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 Scanning dependencies of target mdrun-io-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 83%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-coordination-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/periodicactions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 84%] Built target mdrun-tpi-test /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxapi-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/coordinateio/tests/testmodule.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 85%] Built target options-test /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxapi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/restraint.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 85%] Built target mdrun-modules-test /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp/workflow/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread Scanning dependencies of target workflow-details-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/system.cpp [ 87%] Built target math-test /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp/workflow/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color= Scanning dependencies of target workflow-details-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/swapcoords.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 88%] Built target coordinateio-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/version.cpp Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/version.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 89%] Built target simd-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 89%] Built target workflow-details-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/src/api/cpp -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 89%] Built target mdrun-mpi-coordination-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/readinp.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 90%] Built target workflow-details-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 90%] Built target mdrun-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/tests -I/build/reproducible-path/gromacs-2020.6/src/api/cpp/include -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/api/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 91%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/rerun.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 91%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/multisimtest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp [ 92%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp [ 94%] Built target fileio-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/arraydata.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 95%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 96%] Built target mdrun-io-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/sasa.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 96%] Built target gmxapi-mpi-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/select.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 97%] Built target mdrun-mpi-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/basic-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 97%] Built target mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 97%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 98%] Built target commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [100%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [100%] Built target selection-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2020.6/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i i386 ) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2020.6/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2020.6/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2020.6/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2020.6/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2020.6/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (4 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnys 1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (5 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (8 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (0 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (9 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (18 ms total) 1: [ PASSED ] 59 tests. 1/54 Test #1: TestUtilsUnitTests .................. Passed 0.03 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (4 ms) 2: [----------] 1 test from MpiSelfTest (4 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (4 ms total) 2: [ PASSED ] 1 test. 2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.02 sec test 3 Start 3: UtilityUnitTests 3: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 3: Test timeout computed to be: 30 3: [==========] Running 347 tests from 56 test cases. 3: [----------] Global test environment set-up. 3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.Move 3: [ OK ] AllocatorTest/0.Move (0 ms) 3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/0 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.Move 3: [ OK ] AllocatorTest/1.Move (0 ms) 3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/1 (1 ms total) 3: 3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.Move 3: [ OK ] AllocatorTest/2.Move (0 ms) 3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/2 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.Move 3: [ OK ] AllocatorTest/3.Move (0 ms) 3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/3 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (8 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.Move 3: [ OK ] AllocatorTest/4.Move (0 ms) 3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/4 (8 ms total) 3: 3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.Move 3: [ OK ] AllocatorTest/5.Move (0 ms) 3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/5 (1 ms total) 3: 3: [----------] 1 test from AllocatorUntypedTest 3: [ RUN ] AllocatorUntypedTest.Comparison 3: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 3: [----------] 1 test from AllocatorUntypedTest (0 ms total) 3: 3: [----------] 1 test from EmptyArrayRefTest 3: [ RUN ] EmptyArrayRefTest.IsEmpty 3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyArrayRefTest (0 ms total) 3: 3: [----------] 1 test from EmptyConstArrayRefTest 3: [ RUN ] EmptyConstArrayRefTest.IsEmpty 3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 3: 3: [----------] 2 tests from CStringUtilityTest 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 3: [----------] 2 tests from CStringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from DefaultInitializationAllocator 3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 3: 3: [----------] 4 tests from EnumerationHelpersTest 3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 3: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 3: 3: [----------] 9 tests from FixedCapacityVectorTest 3: [ RUN ] FixedCapacityVectorTest.IsEmpty 3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PushWorks 3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PopWorks 3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ClearWorks 3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.AtThrows 3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 3: [ RUN ] FixedCapacityVectorTest.IteratorWorks 3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 3: [----------] 9 tests from FixedCapacityVectorTest (1 ms total) 3: 3: [----------] 5 tests from InMemorySerializerTest 3: [ RUN ] InMemorySerializerTest.Roundtrip 3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SizeIsCorrect 3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 3: [----------] 5 tests from InMemorySerializerTest (0 ms total) 3: 3: [----------] 4 tests from KeyValueTreeSerializerTest 3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 3: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 3: 3: [----------] 6 tests from TreeValueTransformTest 3: [ RUN ] TreeValueTransformTest.SimpleTransforms 3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromString 3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 3: [ RUN ] TreeValueTransformTest.ScopedTransformRules 3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 3: [----------] 6 tests from TreeValueTransformTest (1 ms total) 3: 3: [----------] 1 test from TreeValueTransformErrorTest 3: [ RUN ] TreeValueTransformErrorTest.ConversionError 3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 3: 3: [----------] 7 tests from LoggerTest 3: [ RUN ] LoggerTest.EmptyLoggerWorks 3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToStream 3: [ OK ] LoggerTest.LogsToStream (0 ms) 3: [ RUN ] LoggerTest.LogsToFile 3: [ OK ] LoggerTest.LogsToFile (0 ms) 3: [ RUN ] LoggerTest.LevelFilteringWorks 3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleStreams 3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleFiles 3: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms) 3: [ RUN ] LoggerTest.LogsToStreamAndFile 3: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 3: [----------] 7 tests from LoggerTest (1 ms total) 3: 3: [----------] 4 tests from MutexBasicTest 3: [ RUN ] MutexBasicTest.CanBeMade 3: [ OK ] MutexBasicTest.CanBeMade (0 ms) 3: [ RUN ] MutexBasicTest.CanBeLocked 3: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeTryLocked 3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 3: [----------] 4 tests from MutexBasicTest (0 ms total) 3: 3: [----------] 3 tests from MutexTaskTest 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (11 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (12 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 3: [----------] 3 tests from MutexTaskTest (23 ms total) 3: 3: [----------] 2 tests from PathTest 3: [ RUN ] PathTest.StripSourcePrefixWorks 3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 3: [ RUN ] PathTest.SearchOperationsWork 3: [ OK ] PathTest.SearchOperationsWork (1 ms) 3: [----------] 2 tests from PathTest (1 ms total) 3: 3: [----------] 2 tests from PhysicalNodeCommunicatorTest 3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 3: 3: [----------] 9 tests from StringUtilityTest 3: [ RUN ] StringUtilityTest.StartsWith 3: [ OK ] StringUtilityTest.StartsWith (0 ms) 3: [ RUN ] StringUtilityTest.EndsWith 3: [ OK ] StringUtilityTest.EndsWith (0 ms) 3: [ RUN ] StringUtilityTest.StripSuffixIfPresent 3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 3: [ RUN ] StringUtilityTest.StripString 3: [ OK ] StringUtilityTest.StripString (0 ms) 3: [ RUN ] StringUtilityTest.SplitString 3: [ OK ] StringUtilityTest.SplitString (0 ms) 3: [ RUN ] StringUtilityTest.SplitDelimitedString 3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 3: [----------] 9 tests from StringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from FormatStringTest 3: [ RUN ] FormatStringTest.HandlesBasicFormatting 3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 3: [ RUN ] FormatStringTest.HandlesLongStrings 3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 3: [----------] 2 tests from FormatStringTest (0 ms total) 3: 3: [----------] 1 test from StringFormatterTest 3: [ RUN ] StringFormatterTest.HandlesBasicFormatting 3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 3: [----------] 1 test from StringFormatterTest (0 ms total) 3: 3: [----------] 1 test from formatAndJoinTest 3: [ RUN ] formatAndJoinTest.Works 3: [ OK ] formatAndJoinTest.Works (0 ms) 3: [----------] 1 test from formatAndJoinTest (0 ms total) 3: 3: [----------] 1 test from JoinStringsTest 3: [ RUN ] JoinStringsTest.Works 3: [ OK ] JoinStringsTest.Works (0 ms) 3: [----------] 1 test from JoinStringsTest (0 ms total) 3: 3: [----------] 6 tests from ReplaceAllTest 3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesNoMatches 3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 3: [----------] 6 tests from ReplaceAllTest (0 ms total) 3: 3: [----------] 10 tests from TextLineWrapperTest 3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectly 3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndent 3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (1 ms) 3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 3: [----------] 10 tests from TextLineWrapperTest (1 ms total) 3: 3: [----------] 6 tests from TextWriterTest 3: [ RUN ] TextWriterTest.WritesLines 3: [ OK ] TextWriterTest.WritesLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInParts 3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 3: [ RUN ] TextWriterTest.WritesWrappedLines 3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 3: [ RUN ] TextWriterTest.TracksNewlines 3: [ OK ] TextWriterTest.TracksNewlines (0 ms) 3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 3: [----------] 6 tests from TextWriterTest (0 ms total) 3: 3: [----------] 1 test from TypeTraitsTest 3: [ RUN ] TypeTraitsTest.IsIntegralConstant 3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 3: [----------] 1 test from TypeTraitsTest (0 ms total) 3: 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 3: 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (14 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (12 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (12 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (12 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (12 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (12 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (74 ms total) 3: 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 347 tests from 56 test cases ran. (114 ms total) 3: [ PASSED ] 347 tests. 3/54 Test #3: UtilityUnitTests .................... Passed 0.17 sec test 4 Start 4: UtilityMpiUnitTests 4: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 4: Test timeout computed to be: 30 4: [==========] Running 2 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from PhysicalNodeCommunicatorTest 4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (32 ms) 4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (36 ms) 4: [----------] 2 tests from PhysicalNodeCommunicatorTest (68 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test case ran. (69 ms total) 4: [ PASSED ] 2 tests. 4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.10 sec test 5 Start 5: MdlibUnitTest 5: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 187 tests from 13 test cases. 5: [----------] Global test environment set-up. 5: [----------] 1 test from VerletBufferConstraintTest 5: [ RUN ] VerletBufferConstraintTest.EqualMasses 5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 5: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 5: 5: [----------] 2 tests from PrEbinTest 5: [ RUN ] PrEbinTest.HandlesAverages 5: [ OK ] PrEbinTest.HandlesAverages (0 ms) 5: [ RUN ] PrEbinTest.HandlesEmptyAverages 5: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 5: [----------] 2 tests from PrEbinTest (0 ms total) 5: 5: [----------] 4 tests from ShakeTest 5: [ RUN ] ShakeTest.ConstrainsOneBond 5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 5: [----------] 4 tests from ShakeTest (1 ms total) 5: 5: [----------] 1 test from NullSignalTest 5: [ RUN ] NullSignalTest.NullSignallerWorks 5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 5: [----------] 1 test from NullSignalTest (0 ms total) 5: 5: [----------] 7 tests from SignalTest 5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 5: [----------] 7 tests from SignalTest (0 ms total) 5: 5: [----------] 9 tests from UpdateGroups 5: [ RUN ] UpdateGroups.ethaneUA 5: [ OK ] UpdateGroups.ethaneUA (0 ms) 5: [ RUN ] UpdateGroups.methane 5: [ OK ] UpdateGroups.methane (0 ms) 5: [ RUN ] UpdateGroups.ethane 5: [ OK ] UpdateGroups.ethane (0 ms) 5: [ RUN ] UpdateGroups.butaneUA 5: [ OK ] UpdateGroups.butaneUA (0 ms) 5: [ RUN ] UpdateGroups.waterThreeSite 5: [ OK ] UpdateGroups.waterThreeSite (0 ms) 5: [ RUN ] UpdateGroups.waterFourSite 5: [ OK ] UpdateGroups.waterFourSite (0 ms) 5: [ RUN ] UpdateGroups.fourAtomsWithSettle 5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 5: [ RUN ] UpdateGroups.waterFlexAngle 5: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 5: [ RUN ] UpdateGroups.twoMoltypes 5: [ OK ] UpdateGroups.twoMoltypes (0 ms) 5: [----------] 9 tests from UpdateGroups (0 ms total) 5: 5: [----------] 1 test from UpdateGroupsCog 5: [ RUN ] UpdateGroupsCog.ComputesCogs 5: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 5: [----------] 1 test from UpdateGroupsCog (0 ms total) 5: 5: [----------] 84 tests from WithParameters/ConstraintsTest 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms) 5: [----------] 84 tests from WithParameters/ConstraintsTest (3 ms total) 5: 5: [----------] 11 tests from WithParameters/EnergyOutputTest 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (10 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 5: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (17 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (10 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 5: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (2 ms) 5: [----------] 11 tests from WithParameters/EnergyOutputTest (53 ms total) 5: 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (4 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (5 ms total) 5: 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 5: 5: [----------] 16 tests from WithParameters/LeapFrogTest 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (9 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (9 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (5 ms) 5: [----------] 16 tests from WithParameters/LeapFrogTest (36 ms total) 5: 5: [----------] 13 tests from WithParameters/SettleTest 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 5: [----------] 13 tests from WithParameters/SettleTest (7 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 187 tests from 13 test cases ran. (105 ms total) 5: [ PASSED ] 187 tests. 5/54 Test #5: MdlibUnitTest ....................... Passed 0.16 sec test 6 Start 6: AppliedForcesUnitTest 6: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 6: Test timeout computed to be: 30 6: [==========] Running 20 tests from 4 test cases. 6: [----------] Global test environment set-up. 6: [----------] 2 tests from DensityFittingTest 6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (4 ms) 6: [ RUN ] DensityFittingTest.SingleAtom 6: [ OK ] DensityFittingTest.SingleAtom (1 ms) 6: [----------] 2 tests from DensityFittingTest (5 ms total) 6: 6: [----------] 8 tests from DensityFittingOptionsTest 6: [ RUN ] DensityFittingOptionsTest.DefaultParameters 6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 6: [ RUN ] DensityFittingOptionsTest.KvtToInternal 6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 6: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 6: 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest 6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (1 ms total) 6: 6: [----------] 3 tests from ElectricFieldTest 6: [ RUN ] ElectricFieldTest.Static 6: [ OK ] ElectricFieldTest.Static (0 ms) 6: [ RUN ] ElectricFieldTest.Oscillating 6: [ OK ] ElectricFieldTest.Oscillating (0 ms) 6: [ RUN ] ElectricFieldTest.Pulsed 6: [ OK ] ElectricFieldTest.Pulsed (0 ms) 6: [----------] 3 tests from ElectricFieldTest (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 20 tests from 4 test cases ran. (6 ms total) 6: [ PASSED ] 20 tests. 6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.04 sec test 7 Start 7: CommandLineUnitTests 7: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 59 tests from 7 test cases. 7: [----------] Global test environment set-up. 7: [----------] 3 tests from CommandLineHelpModuleTest 7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 7: [----------] 3 tests from CommandLineHelpModuleTest (2 ms total) 7: 7: [----------] 7 tests from CommandLineHelpWriterTest 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 7: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 7: 7: [----------] 6 tests from CommandLineModuleManagerTest 7: [ RUN ] CommandLineModuleManagerTest.RunsModule 7: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 7: [----------] 6 tests from CommandLineModuleManagerTest (1 ms total) 7: 7: [----------] 13 tests from CommandLineParserTest 7: [ RUN ] CommandLineParserTest.HandlesSingleValues 7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesString 7: [ OK ] CommandLineParserTest.HandlesString (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 7: [----------] 13 tests from CommandLineParserTest (0 ms total) 7: 7: [----------] 6 tests from CommandLineProgramContextTest 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (4 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (1 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 7: [----------] 6 tests from CommandLineProgramContextTest (5 ms total) 7: 7: [----------] 3 tests from OutputNamesTest 7: [ RUN ] OutputNamesTest.CanBeSuffixed 7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 7: [----------] 3 tests from OutputNamesTest (0 ms total) 7: 7: [----------] 21 tests from ParseCommonArgsTest 7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 7: [----------] 21 tests from ParseCommonArgsTest (1 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 59 tests from 7 test cases ran. (10 ms total) 7: [ PASSED ] 59 tests. 7/54 Test #7: CommandLineUnitTests ................ Passed 0.04 sec test 8 Start 8: DomDecTests 8: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/DomDecTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 9 tests from 2 test cases. 8: [----------] Global test environment set-up. 8: [----------] 7 tests from HashedMap 8: [ RUN ] HashedMap.InsertsFinds 8: [ OK ] HashedMap.InsertsFinds (0 ms) 8: [ RUN ] HashedMap.NegativeKeysWork 8: [ OK ] HashedMap.NegativeKeysWork (0 ms) 8: [ RUN ] HashedMap.InsertsErases 8: [ OK ] HashedMap.InsertsErases (0 ms) 8: [ RUN ] HashedMap.InsertsOrAssigns 8: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 8: [ RUN ] HashedMap.Clears 8: [ OK ] HashedMap.Clears (0 ms) 8: [ RUN ] HashedMap.LinkedEntries 8: [ OK ] HashedMap.LinkedEntries (8 ms) 8: [ RUN ] HashedMap.ResizesTable 8: [ OK ] HashedMap.ResizesTable (0 ms) 8: [----------] 7 tests from HashedMap (8 ms total) 8: 8: [----------] 2 tests from LocalAtomSetManager 8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 8: [----------] 2 tests from LocalAtomSetManager (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 9 tests from 2 test cases ran. (8 ms total) 8: [ PASSED ] 9 tests. 8/54 Test #8: DomDecTests ......................... Passed 0.04 sec test 9 Start 9: EwaldUnitTests 9: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 257 tests from 10 test cases. 9: [----------] Global test environment set-up. 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (12 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms) 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (14 ms total) 9: 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (4 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (16 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (11 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (15 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (24 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (15 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (15 ms) 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (176 ms total) 9: 9: [----------] 144 tests from SaneInput/PmeGatherTest 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (13 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (13 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (0 ms) 9: [----------] 144 tests from SaneInput/PmeGatherTest (135 ms total) 9: 9: [----------] 16 tests from SaneInput/PmeSolveTest 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (9 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (9 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (9 ms) 9: [----------] 16 tests from SaneInput/PmeSolveTest (44 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (7 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (9 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (10 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (27 ms total) 9: 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (10 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (10 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (2 ms) 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (35 ms total) 9: 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (11 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (9 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (34 ms total) 9: 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (9 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (10 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (45 ms total) 9: 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (11 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (12 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (13 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (14 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (12 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (13 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (5 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (14 ms) 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (113 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 257 tests from 10 test cases ran. (780 ms total) 9: [ PASSED ] 257 tests. 9/54 Test #9: EwaldUnitTests ...................... Passed 0.89 sec test 10 Start 10: FFTUnitTests 10: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 14 tests from 4 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from ManyFFTTest 10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (25 ms) 10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (56 ms) 10: [----------] 2 tests from ManyFFTTest (82 ms total) 10: 10: [----------] 1 test from FFTTest 10: [ RUN ] FFTTest.Real2DLength18_15Test 10: [ OK ] FFTTest.Real2DLength18_15Test (21 ms) 10: [----------] 1 test from FFTTest (21 ms total) 10: 10: [----------] 1 test from FFFTest3D 10: [ RUN ] FFFTest3D.Real5_6_9 10: [ OK ] FFFTest3D.Real5_6_9 (2 ms) 10: [----------] 1 test from FFFTest3D (2 ms total) 10: 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (2 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (12 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (3 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (32 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (37 ms) 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (91 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 14 tests from 4 test cases ran. (196 ms total) 10: [ PASSED ] 14 tests. 10/54 Test #10: FFTUnitTests ........................ Passed 0.24 sec test 11 Start 11: GpuUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 62 tests from 20 test cases. 11: [----------] Global test environment set-up. 11: [----------] 2 tests from ClfftInitializer 11: [ RUN ] ClfftInitializer.SingleInitializationWorks 11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 11: [ RUN ] ClfftInitializer.TwoInitializationsWork 11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 11: [----------] 2 tests from ClfftInitializer (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Swap 11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Comparison 11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Swap 11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Comparison 11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Swap 11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Comparison 11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Swap 11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Comparison 11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (1 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (1 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 11: 11: [----------] 1 test from HostAllocatorUntypedTest 11: [ RUN ] HostAllocatorUntypedTest.Comparison 11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/3 (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 62 tests from 20 test cases ran. (1 ms total) 11: [ PASSED ] 62 tests. 11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.04 sec test 12 Start 12: HardwareUnitTests 12: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 4 tests from 1 test case. 12: [----------] Global test environment set-up. 12: [----------] 4 tests from HardwareTopologyTest 12: [ RUN ] HardwareTopologyTest.Execute 12: [ OK ] HardwareTopologyTest.Execute (103 ms) 12: [ RUN ] HardwareTopologyTest.HwlocExecute 12: [ OK ] HardwareTopologyTest.HwlocExecute (128 ms) 12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (128 ms) 12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (119 ms) 12: [----------] 4 tests from HardwareTopologyTest (479 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 4 tests from 1 test case ran. (479 ms total) 12: [ PASSED ] 4 tests. 12/54 Test #12: HardwareUnitTests ................... Passed 0.51 sec test 13 Start 13: MathUnitTests 13: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 204 tests from 29 test cases. 13: [----------] Global test environment set-up. 13: [----------] 1 test from EmptyArrayRefWithPaddingTest 13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (1 ms total) 13: 13: [----------] 8 tests from TranslateAndScaleTest 13: [ RUN ] TranslateAndScaleTest.identityTransformation 13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingIdentity 13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 13: [----------] 8 tests from TranslateAndScaleTest (0 ms total) 13: 13: [----------] 12 tests from DensitySimilarityTest 13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (1 ms) 13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (29 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (28 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (23 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 13: [----------] 12 tests from DensitySimilarityTest (81 ms total) 13: 13: [----------] 6 tests from StructureSimilarityTest 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 13: [----------] 6 tests from StructureSimilarityTest (0 ms total) 13: 13: [----------] 8 tests from ExponentialMovingAverage 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 13: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 13: 13: [----------] 21 tests from FunctionTest 13: [ RUN ] FunctionTest.StaticLog2 13: [ OK ] FunctionTest.StaticLog2 (0 ms) 13: [ RUN ] FunctionTest.Log2I32Bit 13: [ OK ] FunctionTest.Log2I32Bit (0 ms) 13: [ RUN ] FunctionTest.Log2I64Bit 13: [ OK ] FunctionTest.Log2I64Bit (0 ms) 13: [ RUN ] FunctionTest.GreatestCommonDivisor 13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 13: [ RUN ] FunctionTest.InvsqrtFloat 13: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvsqrtDouble 13: [ OK ] FunctionTest.InvsqrtDouble (1 ms) 13: [ RUN ] FunctionTest.InvsqrtInteger 13: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 13: [ RUN ] FunctionTest.InvcbrtFloat 13: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvcbrtDouble 13: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvcbrtInteger 13: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 13: [ RUN ] FunctionTest.SixthrootFloat 13: [ OK ] FunctionTest.SixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.SixthrootDouble 13: [ OK ] FunctionTest.SixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.SixthrootInteger 13: [ OK ] FunctionTest.SixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootFloat 13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootDouble 13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootInteger 13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.Powers 13: [ OK ] FunctionTest.Powers (0 ms) 13: [ RUN ] FunctionTest.ErfInvFloat 13: [ OK ] FunctionTest.ErfInvFloat (0 ms) 13: [ RUN ] FunctionTest.ErfInvDouble 13: [ OK ] FunctionTest.ErfInvDouble (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 13: [----------] 21 tests from FunctionTest (2 ms total) 13: 13: [----------] 4 tests from GaussianOn1DLattice 13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 13: [ RUN ] GaussianOn1DLattice.isCorrect 13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 13: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 13: 13: [----------] 9 tests from GaussTransformTest 13: [ RUN ] GaussTransformTest.isZeroUponConstruction 13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 13: [ RUN ] GaussTransformTest.view 13: [ OK ] GaussTransformTest.view (0 ms) 13: [----------] 9 tests from GaussTransformTest (0 ms total) 13: 13: [----------] 3 tests from DensityFittingForce 13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 13: [ RUN ] DensityFittingForce.pullsTowardsDerivative 13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 13: [----------] 3 tests from DensityFittingForce (0 ms total) 13: 13: [----------] 2 tests from InvertMatrixTest 13: [ RUN ] InvertMatrixTest.IdentityIsImpotent 13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertMatrixTest.ComputesInverse 13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 13: [----------] 2 tests from InvertMatrixTest (0 ms total) 13: 13: [----------] 2 tests from InvertBoxMatrixTest 13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 13: 13: [----------] 15 tests from MatrixTest 13: [ RUN ] MatrixTest.canSetFromArray 13: [ OK ] MatrixTest.canSetFromArray (0 ms) 13: [ RUN ] MatrixTest.canSetStaticallyFromList 13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 13: [ RUN ] MatrixTest.canConstructAndFill 13: [ OK ] MatrixTest.canConstructAndFill (0 ms) 13: [ RUN ] MatrixTest.canSetValues 13: [ OK ] MatrixTest.canSetValues (0 ms) 13: [ RUN ] MatrixTest.canCopyAssign 13: [ OK ] MatrixTest.canCopyAssign (0 ms) 13: [ RUN ] MatrixTest.canSwap 13: [ OK ] MatrixTest.canSwap (0 ms) 13: [ RUN ] MatrixTest.staticMultiDimArrayExtent 13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MatrixTest.determinantWorks 13: [ OK ] MatrixTest.determinantWorks (0 ms) 13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 13: [ RUN ] MatrixTest.traceWorks 13: [ OK ] MatrixTest.traceWorks (0 ms) 13: [ RUN ] MatrixTest.transposeWorks 13: [ OK ] MatrixTest.transposeWorks (0 ms) 13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 13: [ RUN ] MatrixTest.canFillLegacyMatrix 13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 13: [----------] 15 tests from MatrixTest (0 ms total) 13: 13: [----------] 25 tests from MultiDimArrayTest 13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapStatic 13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapDynamic 13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToView 13: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToConstView 13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 13: [ RUN ] MultiDimArrayTest.viewBegin 13: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.viewEnd 13: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstBegin 13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstEnd 13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 13: [----------] 25 tests from MultiDimArrayTest (1 ms total) 13: 13: [----------] 4 tests from MultiDimArrayToMdSpanTest 13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanCopyAssign 13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanMoveAssign 13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanSwap 13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanCopyAssign 13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanMoveAssign 13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanSwap 13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanCopyAssign 13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanMoveAssign 13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanSwap 13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanCopyAssign 13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanMoveAssign 13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanSwap 13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanCopyAssign 13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanMoveAssign 13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanSwap 13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanCopyAssign 13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanMoveAssign 13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanSwap 13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanCopyAssign 13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanMoveAssign 13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanSwap 13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanCopyAssign 13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanMoveAssign 13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanSwap 13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanCopyAssign 13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanMoveAssign 13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanSwap 13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanCopyAssign 13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanMoveAssign 13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanSwap 13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 13: 13: [----------] 37 tests from RVecTest 13: [ RUN ] RVecTest.CanBeStoredInVector 13: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAsMutable_rvec 13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Array 13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 13: [ RUN ] RVecTest.CanAddRVecToRvec 13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanAddAssignRVecToRvec 13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractRVecFromRvec 13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanDotProductRVecByRvec 13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanCrossProductRVecByRvec 13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVecInplace 13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 13: [ RUN ] RVecTest.CanScaleRVec 13: [ OK ] RVecTest.CanScaleRVec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVec 13: [ OK ] RVecTest.CanDivideRVec (0 ms) 13: [ RUN ] RVecTest.CanDoUnitvFromRVec 13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanSqLengthOfRVec 13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanLengthOfRVec 13: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToRVec 13: [ OK ] RVecTest.CanCastToRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToDVec 13: [ OK ] RVecTest.CanCastToDVec (0 ms) 13: [ RUN ] RVecTest.CanLeftScalarMultiply 13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanRightScalarMultiply 13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanGetUnitvFromRVec 13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanGetSqLengthOfRVec 13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanGetLengthOfRVec 13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoCrossProductOfRVec 13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoDotProductOfRVec 13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanScaleByVector 13: [ OK ] RVecTest.CanScaleByVector (0 ms) 13: [ RUN ] RVecTest.asIVec 13: [ OK ] RVecTest.asIVec (0 ms) 13: [ RUN ] RVecTest.elementWiseMin 13: [ OK ] RVecTest.elementWiseMin (0 ms) 13: [ RUN ] RVecTest.elementWiseMax 13: [ OK ] RVecTest.elementWiseMax (0 ms) 13: [ RUN ] RVecTest.WorksAs_dvec_Reference 13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_ivec_Reference 13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Reference 13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 13: [ RUN ] RVecTest.CopyConstructorWorks 13: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 13: [ RUN ] RVecTest.CopyAssignmentWorks 13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] RVecTest.MoveConstructorWorks 13: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 13: [ RUN ] RVecTest.MoveAssignmentWorks 13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 13: [----------] 37 tests from RVecTest (1 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 204 tests from 29 test cases ran. (86 ms total) 13: [ PASSED ] 204 tests. 13/54 Test #13: MathUnitTests ....................... Passed 0.11 sec test 14 Start 14: MdrunUtilityUnitTests 14: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 17 tests from 1 test case. 14: [----------] Global test environment set-up. 14: [----------] 17 tests from ThreadAffinityTest 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 14: NOTE: Affinity setting failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (18 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (16 ms) 14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (16 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 14: NOTE: Affinity setting for 1/2 threads failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (16 ms) 14: [----------] 17 tests from ThreadAffinityTest (69 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 17 tests from 1 test case ran. (69 ms total) 14: [ PASSED ] 17 tests. 14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.08 sec test 15 Start 15: MdrunUtilityMpiUnitTests 15: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 13 tests from 2 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from ThreadAffinityMultiRankTest 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (108 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (120 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (56 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (48 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (68 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (68 ms) 15: [----------] 6 tests from ThreadAffinityMultiRankTest (468 ms total) 15: 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (84 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (60 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (100 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (76 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (68 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (88 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (72 ms) 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (548 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 13 tests from 2 test cases ran. (1016 ms total) 15: [ PASSED ] 13 tests. 15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 1.03 sec test 16 Start 16: MDSpanTests 16: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 32 tests from 7 test cases. 16: [----------] Global test environment set-up. 16: [----------] 4 tests from BasicAccessorPolicy 16: [ RUN ] BasicAccessorPolicy.Decay 16: [ OK ] BasicAccessorPolicy.Decay (0 ms) 16: [ RUN ] BasicAccessorPolicy.Access 16: [ OK ] BasicAccessorPolicy.Access (0 ms) 16: [ RUN ] BasicAccessorPolicy.Offset 16: [ OK ] BasicAccessorPolicy.Offset (0 ms) 16: [ RUN ] BasicAccessorPolicy.CopyAccessor 16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 16: [----------] 4 tests from BasicAccessorPolicy (1 ms total) 16: 16: [----------] 4 tests from ExtentsTest 16: [ RUN ] ExtentsTest.Construction 16: [ OK ] ExtentsTest.Construction (0 ms) 16: [ RUN ] ExtentsTest.PurelyStatic 16: [ OK ] ExtentsTest.PurelyStatic (0 ms) 16: [ RUN ] ExtentsTest.RankNought 16: [ OK ] ExtentsTest.RankNought (0 ms) 16: [ RUN ] ExtentsTest.Assignment 16: [ OK ] ExtentsTest.Assignment (0 ms) 16: [----------] 4 tests from ExtentsTest (0 ms total) 16: 16: [----------] 8 tests from MdSpanExtension 16: [ RUN ] MdSpanExtension.SlicingAllStatic 16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingDynamic 16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingAllStatic3D 16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 16: [ RUN ] MdSpanExtension.SlicingEqualsView3D 16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 16: [ RUN ] MdSpanExtension.additionWorks 16: [ OK ] MdSpanExtension.additionWorks (0 ms) 16: [ RUN ] MdSpanExtension.subtractionWorks 16: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 16: [ RUN ] MdSpanExtension.multiplicationWorks 16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 16: [ RUN ] MdSpanExtension.divisionWorks 16: [ OK ] MdSpanExtension.divisionWorks (0 ms) 16: [----------] 8 tests from MdSpanExtension (0 ms total) 16: 16: [----------] 3 tests from LayoutTests 16: [ RUN ] LayoutTests.LayoutRightConstruction 16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 16: [ RUN ] LayoutTests.LayoutRightProperties 16: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 16: [ RUN ] LayoutTests.LayoutRightOperator 16: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 16: [----------] 3 tests from LayoutTests (0 ms total) 16: 16: [----------] 1 test from MdSpanTest 16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 16: [----------] 1 test from MdSpanTest (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/0.Rank 16: [ OK ] MdSpanTest/0.Rank (0 ms) 16: [ RUN ] MdSpanTest/0.DynamicRank 16: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/0.Extents 16: [ OK ] MdSpanTest/0.Extents (0 ms) 16: [ RUN ] MdSpanTest/0.Strides 16: [ OK ] MdSpanTest/0.Strides (0 ms) 16: [ RUN ] MdSpanTest/0.Properties 16: [ OK ] MdSpanTest/0.Properties (0 ms) 16: [ RUN ] MdSpanTest/0.Operator 16: [ OK ] MdSpanTest/0.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/0 (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/1.Rank 16: [ OK ] MdSpanTest/1.Rank (0 ms) 16: [ RUN ] MdSpanTest/1.DynamicRank 16: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/1.Extents 16: [ OK ] MdSpanTest/1.Extents (0 ms) 16: [ RUN ] MdSpanTest/1.Strides 16: [ OK ] MdSpanTest/1.Strides (0 ms) 16: [ RUN ] MdSpanTest/1.Properties 16: [ OK ] MdSpanTest/1.Properties (0 ms) 16: [ RUN ] MdSpanTest/1.Operator 16: [ OK ] MdSpanTest/1.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/1 (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 32 tests from 7 test cases ran. (1 ms total) 16: [ PASSED ] 32 tests. 16/54 Test #16: MDSpanTests ......................... Passed 0.04 sec test 17 Start 17: OnlineHelpUnitTests 17: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 22 tests from 4 test cases. 17: [----------] Global test environment set-up. 17: [----------] 6 tests from TextTableFormatterTest 17: [ RUN ] TextTableFormatterTest.HandlesBasicCase 17: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesIndentation 17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 17: [----------] 6 tests from TextTableFormatterTest (0 ms total) 17: 17: [----------] 3 tests from HelpManagerTest 17: [ RUN ] HelpManagerTest.HandlesRootTopic 17: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 17: [ RUN ] HelpManagerTest.HandlesSubTopics 17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 17: [ RUN ] HelpManagerTest.HandlesInvalidTopics 17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 17: [----------] 3 tests from HelpManagerTest (1 ms total) 17: 17: [----------] 2 tests from HelpTopicFormattingTest 17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 17: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 17: 17: [----------] 11 tests from HelpWriterContextTest 17: [ RUN ] HelpWriterContextTest.FormatsParagraphs 17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralText 17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsBulletList 17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsGridTable 17: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms) 17: [ RUN ] HelpWriterContextTest.FormatsTitles 17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 17: [----------] 11 tests from HelpWriterContextTest (1 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 22 tests from 4 test cases ran. (2 ms total) 17: [ PASSED ] 22 tests. 17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.03 sec test 18 Start 18: OptionsUnitTests 18: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 110 tests from 18 test cases. 18: [----------] Global test environment set-up. 18: [----------] 5 tests from AbstractOptionStorageTest 18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 18: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 18: 18: [----------] 8 tests from FileNameOptionTest 18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 18: [----------] 8 tests from FileNameOptionTest (0 ms total) 18: 18: [----------] 15 tests from FileNameOptionManagerTest 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (1 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 18: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 18: 18: [----------] 1 test from OptionsTest 18: [ RUN ] OptionsTest.FailsOnNonsafeStorage 18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 18: [----------] 1 test from OptionsTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerTest 18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMissingValue 18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesExtraValue 18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesGroups 18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesSections 18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 18: [----------] 9 tests from OptionsAssignerTest (0 ms total) 18: 18: [----------] 4 tests from OptionsAssignerBooleanTest 18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 18: 18: [----------] 13 tests from OptionsAssignerIntegerTest 18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (4 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (1 ms) 18: [----------] 13 tests from OptionsAssignerIntegerTest (5 ms total) 18: 18: [----------] 5 tests from OptionsAssignerDoubleTest 18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerStringTest 18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 18: 18: [----------] 6 tests from OptionsAssignerEnumTest 18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 18: 18: [----------] 8 tests from RepeatingOptionSectionTest 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 18: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 18: 18: [----------] 1 test from TimeUnitManagerTest 18: [ RUN ] TimeUnitManagerTest.BasicOperations 18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 18: [----------] 1 test from TimeUnitManagerTest (0 ms total) 18: 18: [----------] 4 tests from TimeUnitBehaviorTest 18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 18: 18: [----------] 2 tests from TreeValueSupportAssignTest 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 18: 18: [----------] 1 test from TreeValueSupportAssignErrorTest 18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 18: 18: [----------] 5 tests from TreeValueSupportCheckTest 18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 18: 18: [----------] 6 tests from TreeValueSupportAdjustTest 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 18: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 18: 18: [----------] 8 tests from TreeValueSupportTest 18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsInt64Option 18: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsStringOption 18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsFloatOption 18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumOption 18: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 18: [----------] 8 tests from TreeValueSupportTest (1 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 110 tests from 18 test cases ran. (9 ms total) 18: [ PASSED ] 110 tests. 18/54 Test #18: OptionsUnitTests .................... Passed 0.06 sec test 19 Start 19: PbcutilUnitTest 19: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 19: Test timeout computed to be: 30 19: [==========] Running 3 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 1 test from PbcTest 19: [ RUN ] PbcTest.CalcShiftsWorks 19: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 19: [----------] 1 test from PbcTest (0 ms total) 19: 19: [----------] 2 tests from PbcEnumsTest 19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (1 ms) 19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 19: [----------] 2 tests from PbcEnumsTest (1 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 3 tests from 2 test cases ran. (1 ms total) 19: [ PASSED ] 3 tests. 19/54 Test #19: PbcutilUnitTest ..................... Passed 0.04 sec test 20 Start 20: RandomUnitTests 20: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 44 tests from 10 test cases. 20: [----------] Global test environment set-up. 20: [----------] 4 tests from ExponentialDistributionTest 20: [ RUN ] ExponentialDistributionTest.Output 20: [ OK ] ExponentialDistributionTest.Output (0 ms) 20: [ RUN ] ExponentialDistributionTest.Logical 20: [ OK ] ExponentialDistributionTest.Logical (0 ms) 20: [ RUN ] ExponentialDistributionTest.Reset 20: [ OK ] ExponentialDistributionTest.Reset (0 ms) 20: [ RUN ] ExponentialDistributionTest.AltParam 20: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 20: 20: [----------] 4 tests from GammaDistributionTest 20: [ RUN ] GammaDistributionTest.Output 20: [ OK ] GammaDistributionTest.Output (0 ms) 20: [ RUN ] GammaDistributionTest.Logical 20: [ OK ] GammaDistributionTest.Logical (0 ms) 20: [ RUN ] GammaDistributionTest.Reset 20: [ OK ] GammaDistributionTest.Reset (0 ms) 20: [ RUN ] GammaDistributionTest.AltParam 20: [ OK ] GammaDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from GammaDistributionTest (0 ms total) 20: 20: [----------] 4 tests from NormalDistributionTest 20: [ RUN ] NormalDistributionTest.Output 20: [ OK ] NormalDistributionTest.Output (0 ms) 20: [ RUN ] NormalDistributionTest.Logical 20: [ OK ] NormalDistributionTest.Logical (0 ms) 20: [ RUN ] NormalDistributionTest.Reset 20: [ OK ] NormalDistributionTest.Reset (0 ms) 20: [ RUN ] NormalDistributionTest.AltParam 20: [ OK ] NormalDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from NormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from SeedTest 20: [ RUN ] SeedTest.makeRandomSeed 20: [ OK ] SeedTest.makeRandomSeed (1 ms) 20: [----------] 1 test from SeedTest (1 ms total) 20: 20: [----------] 6 tests from TabulatedNormalDistributionTest 20: [ RUN ] TabulatedNormalDistributionTest.Output14 20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Output16 20: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Logical 20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Reset 20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.AltParam 20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 20: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from TabulatedNormalDistributionTableTest 20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (9 ms) 20: [----------] 1 test from TabulatedNormalDistributionTableTest (9 ms total) 20: 20: [----------] 6 tests from ThreeFry2x64Test 20: [ RUN ] ThreeFry2x64Test.Logical 20: [ OK ] ThreeFry2x64Test.Logical (0 ms) 20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms) 20: [ RUN ] ThreeFry2x64Test.Reseed 20: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 20: [ RUN ] ThreeFry2x64Test.Discard 20: [ OK ] ThreeFry2x64Test.Discard (0 ms) 20: [ RUN ] ThreeFry2x64Test.InvalidCounter 20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 20: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 20: 20: [----------] 4 tests from UniformIntDistributionTest 20: [ RUN ] UniformIntDistributionTest.Output 20: [ OK ] UniformIntDistributionTest.Output (0 ms) 20: [ RUN ] UniformIntDistributionTest.Logical 20: [ OK ] UniformIntDistributionTest.Logical (0 ms) 20: [ RUN ] UniformIntDistributionTest.Reset 20: [ OK ] UniformIntDistributionTest.Reset (0 ms) 20: [ RUN ] UniformIntDistributionTest.AltParam 20: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 20: 20: [----------] 5 tests from UniformRealDistributionTest 20: [ RUN ] UniformRealDistributionTest.GenerateCanonical 20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Output 20: [ OK ] UniformRealDistributionTest.Output (0 ms) 20: [ RUN ] UniformRealDistributionTest.Logical 20: [ OK ] UniformRealDistributionTest.Logical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Reset 20: [ OK ] UniformRealDistributionTest.Reset (0 ms) 20: [ RUN ] UniformRealDistributionTest.AltParam 20: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 20: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 20: 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (1 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 44 tests from 10 test cases ran. (12 ms total) 20: [ PASSED ] 44 tests. 20/54 Test #20: RandomUnitTests ..................... Passed 0.06 sec test 21 Start 21: RestraintTests 21: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/RestraintTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 1 test from 1 test case. 21: [----------] Global test environment set-up. 21: [----------] 1 test from RestraintManager 21: [ RUN ] RestraintManager.restraintList 21: [ OK ] RestraintManager.restraintList (0 ms) 21: [----------] 1 test from RestraintManager (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1 test from 1 test case ran. (0 ms total) 21: [ PASSED ] 1 test. 21/54 Test #21: RestraintTests ...................... Passed 0.04 sec test 22 Start 22: TableUnitTests 22: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 20 tests from 2 test cases. 22: [----------] Global test environment set-up. 22: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 22: [ RUN ] SplineTableTest/0.Sinc 22: [ OK ] SplineTableTest/0.Sinc (0 ms) 22: [ RUN ] SplineTableTest/0.LJ12 22: [ OK ] SplineTableTest/0.LJ12 (34 ms) 22: [ RUN ] SplineTableTest/0.PmeCorrection 22: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 22: [ RUN ] SplineTableTest/0.TwoFunctions 22: [ OK ] SplineTableTest/0.TwoFunctions (65 ms) 22: [ RUN ] SplineTableTest/0.ThreeFunctions 22: [ OK ] SplineTableTest/0.ThreeFunctions (73 ms) 22: [ RUN ] SplineTableTest/0.Simd 22: [ OK ] SplineTableTest/0.Simd (7 ms) 22: [ RUN ] SplineTableTest/0.SimdTwoFunctions 22: [ OK ] SplineTableTest/0.SimdTwoFunctions (63 ms) 22: [----------] 10 tests from SplineTableTest/0 (245 ms total) 22: 22: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (9 ms) 22: [ RUN ] SplineTableTest/1.Sinc 22: [ OK ] SplineTableTest/1.Sinc (1 ms) 22: [ RUN ] SplineTableTest/1.LJ12 22: [ OK ] SplineTableTest/1.LJ12 (82 ms) 22: [ RUN ] SplineTableTest/1.PmeCorrection 22: [ OK ] SplineTableTest/1.PmeCorrection (9 ms) 22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/1.TwoFunctions 22: [ OK ] SplineTableTest/1.TwoFunctions (166 ms) 22: [ RUN ] SplineTableTest/1.ThreeFunctions 22: [ OK ] SplineTableTest/1.ThreeFunctions (191 ms) 22: [ RUN ] SplineTableTest/1.Simd 22: [ OK ] SplineTableTest/1.Simd (32 ms) 22: [ RUN ] SplineTableTest/1.SimdTwoFunctions 22: [ OK ] SplineTableTest/1.SimdTwoFunctions (165 ms) 22: [----------] 10 tests from SplineTableTest/1 (658 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 20 tests from 2 test cases ran. (903 ms total) 22: [ PASSED ] 20 tests. 22/54 Test #22: TableUnitTests ...................... Passed 0.95 sec test 23 Start 23: TaskAssignmentUnitTests 23: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 2 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 2 test cases ran. (1 ms total) 23: [ PASSED ] 3 tests. 23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.04 sec test 24 Start 24: TopologyTest 24: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/TopologyTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 11 tests from 3 test cases. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ExclusionBlockTest 24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 24: [ RUN ] ExclusionBlockTest.MergeExclusions 24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 24: [----------] 3 tests from ExclusionBlockTest (0 ms total) 24: 24: [----------] 2 tests from MtopTest 24: [ RUN ] MtopTest.RangeBasedLoop 24: [ OK ] MtopTest.RangeBasedLoop (0 ms) 24: [ RUN ] MtopTest.Operators 24: [ OK ] MtopTest.Operators (0 ms) 24: [----------] 2 tests from MtopTest (0 ms total) 24: 24: [----------] 6 tests from SymtabTest 24: [ RUN ] SymtabTest.EmptyOnOpen 24: [ OK ] SymtabTest.EmptyOnOpen (0 ms) 24: [ RUN ] SymtabTest.AddSingleEntry 24: [ OK ] SymtabTest.AddSingleEntry (0 ms) 24: [ RUN ] SymtabTest.AddTwoDistinctEntries 24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms) 24: [ RUN ] SymtabTest.TryToAddDuplicates 24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms) 24: [ RUN ] SymtabTest.AddLargeNumberOfEntries 24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms) 24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable 24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms) 24: [----------] 6 tests from SymtabTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 11 tests from 3 test cases ran. (0 ms total) 24: [ PASSED ] 11 tests. 24/54 Test #24: TopologyTest ........................ Passed 0.02 sec test 25 Start 25: PullTest 25: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/PullTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 5 tests from 1 test case. 25: [----------] Global test environment set-up. 25: [----------] 5 tests from PullTest 25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 25: [----------] 5 tests from PullTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 5 tests from 1 test case ran. (0 ms total) 25: [ PASSED ] 5 tests. 25/54 Test #25: PullTest ............................ Passed 0.02 sec test 26 Start 26: AwhTest 26: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/AwhTest.xml" 26: Test timeout computed to be: 30 26: [==========] Running 12 tests from 4 test cases. 26: [----------] Global test environment set-up. 26: [----------] 1 test from BiasTest 26: [ RUN ] BiasTest.DetectsCovering 26: [ OK ] BiasTest.DetectsCovering (0 ms) 26: [----------] 1 test from BiasTest (0 ms total) 26: 26: [----------] 1 test from gridTest 26: [ RUN ] gridTest.neighborhood 26: [ OK ] gridTest.neighborhood (3 ms) 26: [----------] 1 test from gridTest (3 ms total) 26: 26: [----------] 8 tests from WithParameters/BiasTest 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) 26: [----------] 8 tests from WithParameters/BiasTest (3 ms total) 26: 26: [----------] 2 tests from WithParameters/BiasStateTest 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms) 26: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 12 tests from 4 test cases ran. (8 ms total) 26: [ PASSED ] 12 tests. 26/54 Test #26: AwhTest ............................. Passed 0.02 sec test 27 Start 27: SimdUnitTests 27: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 247 tests from 19 test cases. 27: [----------] Global test environment set-up. 27: [----------] 6 tests from SimdBootstrapTest 27: [ RUN ] SimdBootstrapTest.loadStore 27: [ OK ] SimdBootstrapTest.loadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.loadU 27: [ OK ] SimdBootstrapTest.loadU (0 ms) 27: [ RUN ] SimdBootstrapTest.storeU 27: [ OK ] SimdBootstrapTest.storeU (0 ms) 27: [ RUN ] SimdBootstrapTest.loadStoreI 27: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 27: [ RUN ] SimdBootstrapTest.loadUI 27: [ OK ] SimdBootstrapTest.loadUI (0 ms) 27: [ RUN ] SimdBootstrapTest.storeUI 27: [ OK ] SimdBootstrapTest.storeUI (0 ms) 27: [----------] 6 tests from SimdBootstrapTest (0 ms total) 27: 27: [----------] 1 test from SimdTest 27: [ RUN ] SimdTest.GmxAligned 27: [ OK ] SimdTest.GmxAligned (0 ms) 27: [----------] 1 test from SimdTest (0 ms total) 27: 27: [----------] 42 tests from SimdFloatingpointTest 27: [ RUN ] SimdFloatingpointTest.setZero 27: [ OK ] SimdFloatingpointTest.setZero (0 ms) 27: [ RUN ] SimdFloatingpointTest.set 27: [ OK ] SimdFloatingpointTest.set (0 ms) 27: [ RUN ] SimdFloatingpointTest.add 27: [ OK ] SimdFloatingpointTest.add (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskAdd 27: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 27: [ RUN ] SimdFloatingpointTest.sub 27: [ OK ] SimdFloatingpointTest.sub (0 ms) 27: [ RUN ] SimdFloatingpointTest.mul 27: [ OK ] SimdFloatingpointTest.mul (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzMul 27: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 27: [ RUN ] SimdFloatingpointTest.fma 27: [ OK ] SimdFloatingpointTest.fma (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzFma 27: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fms 27: [ OK ] SimdFloatingpointTest.fms (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnma 27: [ OK ] SimdFloatingpointTest.fnma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnms 27: [ OK ] SimdFloatingpointTest.fnms (0 ms) 27: [ RUN ] SimdFloatingpointTest.abs 27: [ OK ] SimdFloatingpointTest.abs (0 ms) 27: [ RUN ] SimdFloatingpointTest.neg 27: [ OK ] SimdFloatingpointTest.neg (0 ms) 27: [ RUN ] SimdFloatingpointTest.and 27: [ OK ] SimdFloatingpointTest.and (0 ms) 27: [ RUN ] SimdFloatingpointTest.or 27: [ OK ] SimdFloatingpointTest.or (0 ms) 27: [ RUN ] SimdFloatingpointTest.xor 27: [ OK ] SimdFloatingpointTest.xor (0 ms) 27: [ RUN ] SimdFloatingpointTest.andNot 27: [ OK ] SimdFloatingpointTest.andNot (0 ms) 27: [ RUN ] SimdFloatingpointTest.max 27: [ OK ] SimdFloatingpointTest.max (0 ms) 27: [ RUN ] SimdFloatingpointTest.min 27: [ OK ] SimdFloatingpointTest.min (0 ms) 27: [ RUN ] SimdFloatingpointTest.round 27: [ OK ] SimdFloatingpointTest.round (0 ms) 27: [ RUN ] SimdFloatingpointTest.roundMode 27: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 27: [ RUN ] SimdFloatingpointTest.trunc 27: [ OK ] SimdFloatingpointTest.trunc (0 ms) 27: [ RUN ] SimdFloatingpointTest.frexp 27: [ OK ] SimdFloatingpointTest.frexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.ldexp 27: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.rsqrt 27: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRsqrt 27: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.rcp 27: [ OK ] SimdFloatingpointTest.rcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRcp 27: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.selectByNotMask 27: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpNe 27: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLe 27: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLt 27: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 27: [ RUN ] SimdFloatingpointTest.testBits 27: [ OK ] SimdFloatingpointTest.testBits (0 ms) 27: [ RUN ] SimdFloatingpointTest.andB 27: [ OK ] SimdFloatingpointTest.andB (0 ms) 27: [ RUN ] SimdFloatingpointTest.orB 27: [ OK ] SimdFloatingpointTest.orB (0 ms) 27: [ RUN ] SimdFloatingpointTest.anyTrueB 27: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 27: [ RUN ] SimdFloatingpointTest.blend 27: [ OK ] SimdFloatingpointTest.blend (0 ms) 27: [ RUN ] SimdFloatingpointTest.reduce 27: [ OK ] SimdFloatingpointTest.reduce (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 27: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 27: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 27: [----------] 42 tests from SimdFloatingpointTest (1 ms total) 27: 27: [----------] 13 tests from SimdFloatingpointUtilTest 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 27: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 27: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 27: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 27: 27: [----------] 3 tests from SimdVectorOperationsTest 27: [ RUN ] SimdVectorOperationsTest.iprod 27: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 27: [ RUN ] SimdVectorOperationsTest.norm2 27: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 27: [ RUN ] SimdVectorOperationsTest.cprod 27: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 27: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 27: 27: [----------] 56 tests from SimdMathTest 27: [ RUN ] SimdMathTest.generateTestPointsDouble 27: [ OK ] SimdMathTest.generateTestPointsDouble (0 ms) 27: [ RUN ] SimdMathTest.copysign 27: [ OK ] SimdMathTest.copysign (0 ms) 27: [ RUN ] SimdMathTest.invsqrt 27: [ OK ] SimdMathTest.invsqrt (1 ms) 27: [ RUN ] SimdMathTest.maskzInvsqrt 27: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPair 27: [ OK ] SimdMathTest.invsqrtPair (1 ms) 27: [ RUN ] SimdMathTest.sqrt 27: [ OK ] SimdMathTest.sqrt (13 ms) 27: [ RUN ] SimdMathTest.sqrtUnsafe 27: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 27: [ RUN ] SimdMathTest.inv 27: [ OK ] SimdMathTest.inv (1 ms) 27: [ RUN ] SimdMathTest.maskzInv 27: [ OK ] SimdMathTest.maskzInv (0 ms) 27: [ RUN ] SimdMathTest.cbrt 27: [ OK ] SimdMathTest.cbrt (2 ms) 27: [ RUN ] SimdMathTest.invcbrt 27: [ OK ] SimdMathTest.invcbrt (3 ms) 27: [ RUN ] SimdMathTest.log2 27: [ OK ] SimdMathTest.log2 (1 ms) 27: [ RUN ] SimdMathTest.log 27: [ OK ] SimdMathTest.log (0 ms) 27: [ RUN ] SimdMathTest.exp2 27: [ OK ] SimdMathTest.exp2 (5 ms) 27: [ RUN ] SimdMathTest.exp2Unsafe 27: [ OK ] SimdMathTest.exp2Unsafe (1 ms) 27: [ RUN ] SimdMathTest.exp 27: [ OK ] SimdMathTest.exp (6 ms) 27: [ RUN ] SimdMathTest.expUnsafe 27: [ OK ] SimdMathTest.expUnsafe (1 ms) 27: [ RUN ] SimdMathTest.pow 27: [ OK ] SimdMathTest.pow (0 ms) 27: [ RUN ] SimdMathTest.powUnsafe 27: [ OK ] SimdMathTest.powUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erf 27: [ OK ] SimdMathTest.erf (1 ms) 27: [ RUN ] SimdMathTest.erfc 27: [ OK ] SimdMathTest.erfc (3 ms) 27: [ RUN ] SimdMathTest.sin 27: [ OK ] SimdMathTest.sin (3 ms) 27: [ RUN ] SimdMathTest.cos 27: [ OK ] SimdMathTest.cos (2 ms) 27: [ RUN ] SimdMathTest.tan 27: [ OK ] SimdMathTest.tan (3 ms) 27: [ RUN ] SimdMathTest.asin 27: [ OK ] SimdMathTest.asin (1 ms) 27: [ RUN ] SimdMathTest.acos 27: [ OK ] SimdMathTest.acos (2 ms) 27: [ RUN ] SimdMathTest.atan 27: [ OK ] SimdMathTest.atan (1 ms) 27: [ RUN ] SimdMathTest.atan2 27: [ OK ] SimdMathTest.atan2 (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrection 27: [ OK ] SimdMathTest.pmeForceCorrection (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrection 27: [ OK ] SimdMathTest.pmePotentialCorrection (2 ms) 27: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracy 27: [ OK ] SimdMathTest.sqrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.invSingleAccuracy 27: [ OK ] SimdMathTest.invSingleAccuracy (3 ms) 27: [ RUN ] SimdMathTest.cbrtSingleAccuracy 27: [ OK ] SimdMathTest.cbrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 27: [ OK ] SimdMathTest.invcbrtSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.log2SingleAccuracy 27: [ OK ] SimdMathTest.log2SingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.logSingleAccuracy 27: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracy 27: [ OK ] SimdMathTest.exp2SingleAccuracy (4 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 27: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (1 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracy 27: [ OK ] SimdMathTest.expSingleAccuracy (5 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (1 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracy 27: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erfSingleAccuracy 27: [ OK ] SimdMathTest.erfSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.erfcSingleAccuracy 27: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.sinSingleAccuracy 27: [ OK ] SimdMathTest.sinSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.cosSingleAccuracy 27: [ OK ] SimdMathTest.cosSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.tanSingleAccuracy 27: [ OK ] SimdMathTest.tanSingleAccuracy (3 ms) 27: [ RUN ] SimdMathTest.asinSingleAccuracy 27: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.acosSingleAccuracy 27: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atanSingleAccuracy 27: [ OK ] SimdMathTest.atanSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.atan2SingleAccuracy 27: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (1 ms) 27: [----------] 56 tests from SimdMathTest (93 ms total) 27: 27: [----------] 1 test from EmptyArrayRefTest 27: [ RUN ] EmptyArrayRefTest.IsEmpty 27: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 27: [----------] 1 test from EmptyArrayRefTest (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/0.Assignment 27: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/1.Assignment 27: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/0.Basic 27: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/1.Basic 27: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 27: 27: [----------] 23 tests from SimdIntegerTest 27: [ RUN ] SimdIntegerTest.setZero 27: [ OK ] SimdIntegerTest.setZero (0 ms) 27: [ RUN ] SimdIntegerTest.set 27: [ OK ] SimdIntegerTest.set (0 ms) 27: [ RUN ] SimdIntegerTest.add 27: [ OK ] SimdIntegerTest.add (0 ms) 27: [ RUN ] SimdIntegerTest.sub 27: [ OK ] SimdIntegerTest.sub (0 ms) 27: [ RUN ] SimdIntegerTest.mul 27: [ OK ] SimdIntegerTest.mul (0 ms) 27: [ RUN ] SimdIntegerTest.and 27: [ OK ] SimdIntegerTest.and (0 ms) 27: [ RUN ] SimdIntegerTest.andNot 27: [ OK ] SimdIntegerTest.andNot (0 ms) 27: [ RUN ] SimdIntegerTest.or 27: [ OK ] SimdIntegerTest.or (0 ms) 27: [ RUN ] SimdIntegerTest.xor 27: [ OK ] SimdIntegerTest.xor (0 ms) 27: [ RUN ] SimdIntegerTest.extract 27: [ OK ] SimdIntegerTest.extract (0 ms) 27: [ RUN ] SimdIntegerTest.cvtR2I 27: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvttR2I 27: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvtI2R 27: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpLt 27: [ OK ] SimdIntegerTest.cmpLt (0 ms) 27: [ RUN ] SimdIntegerTest.testBits 27: [ OK ] SimdIntegerTest.testBits (0 ms) 27: [ RUN ] SimdIntegerTest.andB 27: [ OK ] SimdIntegerTest.andB (0 ms) 27: [ RUN ] SimdIntegerTest.orB 27: [ OK ] SimdIntegerTest.orB (0 ms) 27: [ RUN ] SimdIntegerTest.anyTrue 27: [ OK ] SimdIntegerTest.anyTrue (0 ms) 27: [ RUN ] SimdIntegerTest.blend 27: [ OK ] SimdIntegerTest.blend (0 ms) 27: [ RUN ] SimdIntegerTest.cvtB2IB 27: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 27: [ RUN ] SimdIntegerTest.cvtIB2B 27: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 27: [----------] 23 tests from SimdIntegerTest (0 ms total) 27: 27: [----------] 41 tests from SimdScalarTest 27: [ RUN ] SimdScalarTest.load 27: [ OK ] SimdScalarTest.load (0 ms) 27: [ RUN ] SimdScalarTest.loadU 27: [ OK ] SimdScalarTest.loadU (0 ms) 27: [ RUN ] SimdScalarTest.store 27: [ OK ] SimdScalarTest.store (0 ms) 27: [ RUN ] SimdScalarTest.storeU 27: [ OK ] SimdScalarTest.storeU (0 ms) 27: [ RUN ] SimdScalarTest.setZero 27: [ OK ] SimdScalarTest.setZero (0 ms) 27: [ RUN ] SimdScalarTest.andNot 27: [ OK ] SimdScalarTest.andNot (0 ms) 27: [ RUN ] SimdScalarTest.fma 27: [ OK ] SimdScalarTest.fma (0 ms) 27: [ RUN ] SimdScalarTest.fms 27: [ OK ] SimdScalarTest.fms (0 ms) 27: [ RUN ] SimdScalarTest.fnma 27: [ OK ] SimdScalarTest.fnma (0 ms) 27: [ RUN ] SimdScalarTest.fnms 27: [ OK ] SimdScalarTest.fnms (0 ms) 27: [ RUN ] SimdScalarTest.maskAdd 27: [ OK ] SimdScalarTest.maskAdd (0 ms) 27: [ RUN ] SimdScalarTest.maskzMul 27: [ OK ] SimdScalarTest.maskzMul (0 ms) 27: [ RUN ] SimdScalarTest.maskzFma 27: [ OK ] SimdScalarTest.maskzFma (0 ms) 27: [ RUN ] SimdScalarTest.abs 27: [ OK ] SimdScalarTest.abs (0 ms) 27: [ RUN ] SimdScalarTest.max 27: [ OK ] SimdScalarTest.max (0 ms) 27: [ RUN ] SimdScalarTest.min 27: [ OK ] SimdScalarTest.min (0 ms) 27: [ RUN ] SimdScalarTest.round 27: [ OK ] SimdScalarTest.round (0 ms) 27: [ RUN ] SimdScalarTest.trunc 27: [ OK ] SimdScalarTest.trunc (0 ms) 27: [ RUN ] SimdScalarTest.reduce 27: [ OK ] SimdScalarTest.reduce (0 ms) 27: [ RUN ] SimdScalarTest.testBits 27: [ OK ] SimdScalarTest.testBits (0 ms) 27: [ RUN ] SimdScalarTest.anyTrue 27: [ OK ] SimdScalarTest.anyTrue (0 ms) 27: [ RUN ] SimdScalarTest.selectByMask 27: [ OK ] SimdScalarTest.selectByMask (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMask 27: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 27: [ RUN ] SimdScalarTest.blend 27: [ OK ] SimdScalarTest.blend (0 ms) 27: [ RUN ] SimdScalarTest.cvtR2I 27: [ OK ] SimdScalarTest.cvtR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvttR2I 27: [ OK ] SimdScalarTest.cvttR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvtI2R 27: [ OK ] SimdScalarTest.cvtI2R (0 ms) 27: [ RUN ] SimdScalarTest.cvtF2D 27: [ OK ] SimdScalarTest.cvtF2D (0 ms) 27: [ RUN ] SimdScalarTest.cvtD2D 27: [ OK ] SimdScalarTest.cvtD2D (0 ms) 27: [ RUN ] SimdScalarTest.loadI 27: [ OK ] SimdScalarTest.loadI (0 ms) 27: [ RUN ] SimdScalarTest.loadUI 27: [ OK ] SimdScalarTest.loadUI (0 ms) 27: [ RUN ] SimdScalarTest.storeI 27: [ OK ] SimdScalarTest.storeI (0 ms) 27: [ RUN ] SimdScalarTest.storeUI 27: [ OK ] SimdScalarTest.storeUI (0 ms) 27: [ RUN ] SimdScalarTest.andNotI 27: [ OK ] SimdScalarTest.andNotI (0 ms) 27: [ RUN ] SimdScalarTest.testBitsI 27: [ OK ] SimdScalarTest.testBitsI (0 ms) 27: [ RUN ] SimdScalarTest.selectByMaskI 27: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMaskI 27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 27: [ RUN ] SimdScalarTest.blendI 27: [ OK ] SimdScalarTest.blendI (0 ms) 27: [ RUN ] SimdScalarTest.cvtB2IB 27: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 27: [ RUN ] SimdScalarTest.cvtIB2B 27: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 27: [ RUN ] SimdScalarTest.expandScalarsToTriplets 27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 27: [----------] 41 tests from SimdScalarTest (0 ms total) 27: 27: [----------] 8 tests from SimdScalarUtilTest 27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 27: [----------] 8 tests from SimdScalarUtilTest (1 ms total) 27: 27: [----------] 37 tests from SimdScalarMathTest 27: [ RUN ] SimdScalarMathTest.copysign 27: [ OK ] SimdScalarMathTest.copysign (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPair 27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdScalarMathTest.inv 27: [ OK ] SimdScalarMathTest.inv (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrt 27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdScalarMathTest.log 27: [ OK ] SimdScalarMathTest.log (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2 27: [ OK ] SimdScalarMathTest.exp2 (0 ms) 27: [ RUN ] SimdScalarMathTest.exp 27: [ OK ] SimdScalarMathTest.exp (0 ms) 27: [ RUN ] SimdScalarMathTest.erf 27: [ OK ] SimdScalarMathTest.erf (0 ms) 27: [ RUN ] SimdScalarMathTest.erfc 27: [ OK ] SimdScalarMathTest.erfc (0 ms) 27: [ RUN ] SimdScalarMathTest.sincos 27: [ OK ] SimdScalarMathTest.sincos (0 ms) 27: [ RUN ] SimdScalarMathTest.sin 27: [ OK ] SimdScalarMathTest.sin (0 ms) 27: [ RUN ] SimdScalarMathTest.cos 27: [ OK ] SimdScalarMathTest.cos (0 ms) 27: [ RUN ] SimdScalarMathTest.tan 27: [ OK ] SimdScalarMathTest.tan (0 ms) 27: [ RUN ] SimdScalarMathTest.asin 27: [ OK ] SimdScalarMathTest.asin (0 ms) 27: [ RUN ] SimdScalarMathTest.acos 27: [ OK ] SimdScalarMathTest.acos (0 ms) 27: [ RUN ] SimdScalarMathTest.atan 27: [ OK ] SimdScalarMathTest.atan (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2 27: [ OK ] SimdScalarMathTest.atan2 (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrection 27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.invSingleAccuracy 27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.logSingleAccuracy 27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.expSingleAccuracy 27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 27: [----------] 37 tests from SimdScalarMathTest (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 247 tests from 19 test cases ran. (95 ms total) 27: [ PASSED ] 247 tests. 27/54 Test #27: SimdUnitTests ....................... Passed 0.14 sec test 28 Start 28: CompatibilityHelpersTests 28: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 28: Test timeout computed to be: 30 28: [==========] Running 170 tests from 12 test cases. 28: [----------] Global test environment set-up. 28: [----------] 45 tests from OptionalTest 28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes 28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructEmpty 28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms) 28: [ RUN ] OptionalTest.CanConstructFromNullopt 28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType 28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral 28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting 28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValue 28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting 28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValue 28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral 28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage 28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral 28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromValue 28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignFromValue 28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanResetContent 28: [ OK ] OptionalTest.CanResetContent (0 ms) 28: [ RUN ] OptionalTest.ProvidesRelationalOperators 28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators 28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.CanProduceHash 28: [ OK ] OptionalTest.CanProduceHash (0 ms) 28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType 28: alignment_of: 1 28: alignment_of: 2 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 16 28: alignment_of: 1 28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms) 28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType 28: sizeof( nonstd::optional_lite::detail::storage_t ): 1 28: sizeof( optional ): 2 (1) 28: sizeof( optional ): 4 (2) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 32 (16) 28: sizeof( optional ): 2 (1) 28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms) 28: [----------] 45 tests from OptionalTest (0 ms total) 28: 28: [----------] 7 tests from MakeOptionalTest 28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] MakeOptionalTest.CanCopyConstruct 28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanMoveConstruct 28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms) 28: [----------] 7 tests from MakeOptionalTest (0 ms total) 28: 28: [----------] 4 tests from OptionalMemberSwapTest 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms) 28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total) 28: 28: [----------] 4 tests from OptionalImplicitValueTest 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms) 28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total) 28: 28: [----------] 20 tests from OptionalIntValueTest 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool 28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (1 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms) 28: [----------] 20 tests from OptionalIntValueTest (1 ms total) 28: 28: [----------] 1 test from NotNullConstruction 28: [ RUN ] NotNullConstruction.Works 28: [ OK ] NotNullConstruction.Works (0 ms) 28: [----------] 1 test from NotNullConstruction (0 ms total) 28: 28: [----------] 1 test from NotNullCasting 28: [ RUN ] NotNullCasting.Works 28: [ OK ] NotNullCasting.Works (0 ms) 28: [----------] 1 test from NotNullCasting (0 ms total) 28: 28: [----------] 1 test from NotNullAssignment 28: [ RUN ] NotNullAssignment.Works 28: [ OK ] NotNullAssignment.Works (0 ms) 28: [----------] 1 test from NotNullAssignment (0 ms total) 28: 28: [----------] 1 test from MakeNotNull 28: [ RUN ] MakeNotNull.Works 28: [ OK ] MakeNotNull.Works (0 ms) 28: [----------] 1 test from MakeNotNull (0 ms total) 28: 28: [----------] 1 test from NotNull 28: [ RUN ] NotNull.WorksInContainers 28: [ OK ] NotNull.WorksInContainers (0 ms) 28: [----------] 1 test from NotNull (0 ms total) 28: 28: [----------] 80 tests from StringViewTest 28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView 28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize 28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromCString 28: [ OK ] StringViewTest.CanConstructFromCString (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.AllowForwardIteration 28: [ OK ] StringViewTest.AllowForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstForwardIteration 28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowReverseIteration 28: [ OK ] StringViewTest.AllowReverseIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstReverseIteration 28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms) 28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize 28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms) 28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty 28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex 28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaAt 28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms) 28: [ RUN ] StringViewTest.CanAccessAllElementsViaData 28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms) 28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr 28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms) 28: [ RUN ] StringViewTest.CanRemovePrefix 28: [ OK ] StringViewTest.CanRemovePrefix (0 ms) 28: [ RUN ] StringViewTest.CanRemoveSuffix 28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms) 28: [ RUN ] StringViewTest.CanSwapWithOtherView 28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms) 28: [ RUN ] StringViewTest.CanCopySubstringWithCopy 28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms) 28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr 28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms) 28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare 28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare 28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (1 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCompareToViews 28: [ OK ] StringViewTest.CanCompareToViews (0 ms) 28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView 28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms) 28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual 28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms) 28: [ RUN ] StringViewTest.CanPrintViewToPutputStream 28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms) 28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms) 28: [----------] 80 tests from StringViewTest (1 ms total) 28: 28: [----------] 5 tests from StringViewExtensionTest 28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString 28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms) 28: [----------] 5 tests from StringViewExtensionTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 170 tests from 12 test cases ran. (3 ms total) 28: [ PASSED ] 170 tests. 28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.07 sec test 29 Start 29: GmxAnaTest 29: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 29: Test timeout computed to be: 600 29: [==========] Running 27 tests from 5 test cases. 29: [----------] Global test environment set-up. 29: [----------] 5 tests from Entropy 29: [ RUN ] Entropy.Schlitter_300_NoLinear 29: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 29: [ RUN ] Entropy.Schlitter_300_Linear 29: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_200_Linear 29: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 29: [----------] 5 tests from Entropy (0 ms total) 29: 29: [----------] 10 tests from MindistTest 29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (1 ms) 29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 2: 'atom3' 29: Selected 3: 'atoms12' 29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (1 ms) 29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (1 ms) 29: [ RUN ] MindistTest.mindistPicksUpContacts 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 29: [ RUN ] MindistTest.ngWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.ngWorks (6 ms) 29: [ RUN ] MindistTest.groupWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 3: 'atoms12' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.groupWorks (1 ms) 29: [ RUN ] MindistTest.maxDistWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 2: 'atom3' 29: Selected 3: 'atoms12' 29: [ OK ] MindistTest.maxDistWorks (0 ms) 29: [ RUN ] MindistTest.noPbcWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.noPbcWorks (1 ms) 29: [ RUN ] MindistTest.resPerTimeWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 3: 'atoms12' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.resPerTimeWorks (5 ms) 29: [ RUN ] MindistTest.matrixWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 5: 'atoms123' 29: Special case: making distance matrix between all atoms in group atoms123 29: [ OK ] MindistTest.matrixWorks (1 ms) 29: [----------] 10 tests from MindistTest (17 ms total) 29: 29: [----------] 3 tests from MsdTest 29: [ RUN ] MsdTest.threeDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.threeDimensionalDiffusion (1 ms) 29: [ RUN ] MsdTest.twoDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.twoDimensionalDiffusion (0 ms) 29: [ RUN ] MsdTest.oneDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.oneDimensionalDiffusion (1 ms) 29: [----------] 3 tests from MsdTest (2 ms total) 29: 29: [----------] 3 tests from MsdMolTest 29: [ RUN ] MsdMolTest.diffMolMassWeighted 29: 29: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to -17057953 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( water) has 15 elements 29: There is one group in the index 29: Split group of 15 atoms into 5 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 6.4731 Std. Dev. = 8.0969 Error = 3.6210 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolMassWeighted (1015 ms) 29: [ RUN ] MsdMolTest.diffMolNonMassWeighted 29: 29: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to -722075813 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( water) has 15 elements 29: There is one group in the index 29: Split group of 15 atoms into 5 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 6.4731 Std. Dev. = 8.0969 Error = 3.6210 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolNonMassWeighted (579 ms) 29: [ RUN ] MsdMolTest.diffMolSelected 29: 29: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to 2130181115 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( mol) has 9 elements 29: There is one group in the index 29: Split group of 9 atoms into 3 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 7.3593 Std. Dev. = 9.7910 Error = 5.6529 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolSelected (703 ms) 29: [----------] 3 tests from MsdMolTest (2297 ms total) 29: 29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: trr version: GMX_trn_file (single precision) 29: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (2 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frames from gro file '', 6 atoms. 29: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 't= 0.00000', 6 atoms 29: Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (2 ms) 29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (8 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 27 tests from 5 test cases ran. (2324 ms total) 29: [ PASSED ] 27 tests. 29/54 Test #29: GmxAnaTest .......................... Passed 2.36 sec test 30 Start 30: GmxPreprocessTests 30: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 30: Test timeout computed to be: 30 30: [==========] Running 51 tests from 9 test cases. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from GenconfTest 30: [ RUN ] GenconfTest.nbox_Works 30: [ OK ] GenconfTest.nbox_Works (0 ms) 30: [ RUN ] GenconfTest.nbox_norenumber_Works 30: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) 30: [ RUN ] GenconfTest.nbox_dist_Works 30: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 30: [ RUN ] GenconfTest.nbox_rot_Works 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 30: [----------] 4 tests from GenconfTest (2 ms total) 30: 30: [----------] 2 tests from GenionTest 30: [ RUN ] GenionTest.HighConcentrationIonPlacement 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 30: buffer. The cluster pair list does have a buffering effect, but choosing 30: a larger rlist might be necessary for good energy conservation. 30: 30: 30: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: Setting the LD random seed to -408946209 30: Generated 331705 of the 331705 non-bonded parameter combinations 30: Generating 1-4 interactions: fudge = 0.5 30: Generated 331705 of the 331705 1-4 parameter combinations 30: Excluding 2 bonded neighbours molecule type 'SOL' 30: Excluding 3 bonded neighbours molecule type 'methane' 30: Number of degrees of freedom in T-Coupling group rest is 1308.00 30: 30: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: You are using a plain Coulomb cut-off, which might produce artifacts. 30: You might want to consider using PME electrostatics. 30: 30: 30: 30: There were 3 notes 30: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 30: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 30: Group 0 ( System) has 653 elements 30: Group 1 ( Water) has 648 elements 30: Group 2 ( SOL) has 648 elements 30: Group 3 ( non-Water) has 5 elements 30: Group 4 ( Other) has 5 elements 30: Group 5 ( METH) has 5 elements 30: Select a group: Number of (3-atomic) solvent molecules: 216 30: Using random seed 1997. 30: Replacing solvent molecule 56 (atom 168) with NA 30: Replacing solvent molecule 120 (atom 360) with NA 30: Replacing solvent molecule 182 (atom 546) with NA 30: Replacing solvent molecule 71 (atom 213) with NA 30: Replacing solvent molecule 189 (atom 567) with CL 30: Replacing solvent molecule 54 (atom 162) with CL 30: Replacing solvent molecule 155 (atom 465) with CL 30: Replacing solvent molecule 99 (atom 297) with CL 30: 30: Analysing residue names: 30: There are: 216 Water residues 30: There are: 1 Other residues 30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 30: This run will generate roughly 0 Mb of data 30: Will try to add 4 NA ions and 4 CL ions. 30: Select a continuous group of solvent molecules 30: Selected 1: 'Water' 30: [ OK ] GenionTest.HighConcentrationIonPlacement (698 ms) 30: [ RUN ] GenionTest.NoIonPlacement 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 30: buffer. The cluster pair list does have a buffering effect, but choosing 30: a larger rlist might be necessary for good energy conservation. 30: 30: 30: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: Setting the LD random seed to -86017 30: Generated 331705 of the 331705 non-bonded parameter combinations 30: Generating 1-4 interactions: fudge = 0.5 30: Generated 331705 of the 331705 1-4 parameter combinations 30: Excluding 2 bonded neighbours molecule type 'SOL' 30: Excluding 3 bonded neighbours molecule type 'methane' 30: Number of degrees of freedom in T-Coupling group rest is 1308.00 30: 30: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: You are using a plain Coulomb cut-off, which might produce artifacts. 30: You might want to consider using PME electrostatics. 30: 30: 30: 30: There were 3 notes 30: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 30: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 30: No ions to add, will just copy input configuration. 30: Analysing residue names: 30: There are: 216 Water residues 30: There are: 1 Other residues 30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 30: This run will generate roughly 0 Mb of data 30: [ OK ] GenionTest.NoIonPlacement (622 ms) 30: [----------] 2 tests from GenionTest (1320 ms total) 30: 30: [----------] 1 test from GenRestrTest 30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 30: 30: Reading structure file 30: Group 0 ( System) has 156 elements 30: Group 1 ( Protein) has 156 elements 30: Group 2 ( Protein-H) has 75 elements 30: Group 3 ( C-alpha) has 10 elements 30: Group 4 ( Backbone) has 30 elements 30: Group 5 ( MainChain) has 40 elements 30: Group 6 ( MainChain+Cb) has 49 elements 30: Group 7 ( MainChain+H) has 52 elements 30: Group 8 ( SideChain) has 104 elements 30: Group 9 ( SideChain-H) has 35 elements 30: Select a group: Select group to position restrain 30: Selected 3: 'C-alpha' 30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (4 ms) 30: [----------] 1 test from GenRestrTest (4 ms total) 30: 30: [----------] 9 tests from PreprocessingAtomTypesTest 30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 30: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 30: 30: [----------] 10 tests from PreprocessingBondAtomTypeTest 30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 30: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 30: 30: [----------] 5 tests from InsertMoleculesTest 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 8 atoms)! 30: 30: Added 1 molecules (out of 1 requested) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 30: 30: Output configuration contains 8 atoms in 4 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (2 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 2 atoms)! 30: Try 2 success (now 4 atoms)! 30: Try 3 success (now 6 atoms)! 30: Try 4 success (now 8 atoms)! 30: Try 5 success (now 10 atoms)! 30: 30: Added 5 molecules (out of 5 requested) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 30: 30: Output configuration contains 10 atoms in 10 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (2 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 8 atoms)! 30: Try 2 success (now 10 atoms)! 30: 30: Added 2 molecules (out of 2 requested) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 30: 30: Output configuration contains 10 atoms in 4 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (12 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 650 atoms)! 30: Try 2 success (now 652 atoms)! 30: Try 3 success (now 654 atoms)! 30: Try 4 success (now 656 atoms)! 30: 30: Added 4 molecules (out of 4 requested) 30: Replaced 8 residues (24 atoms) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 30: 30: Output configuration contains 632 atoms in 212 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (10 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Read 4 positions from file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 30: 30: Try 1 success (now 2 atoms)! 30: Try 2 success (now 4 atoms)! 30: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 30: Try 13 success (now 6 atoms)! 30: 30: Added 3 molecules (out of 4 requested) 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 30: 30: Output configuration contains 6 atoms in 3 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (2 ms) 30: [----------] 5 tests from InsertMoleculesTest (28 ms total) 30: 30: [----------] 14 tests from GetIrTest 30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 30: Ignoring obsolete mdp entry 'title' 30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (11 ms) 30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (10 ms) 30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (3 ms) 30: [ RUN ] GetIrTest.RejectsValueWithoutKey 30: [ OK ] GetIrTest.RejectsValueWithoutKey (9 ms) 30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (13 ms) 30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (3 ms) 30: [ RUN ] GetIrTest.AcceptsEmptyLines 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsEmptyLines (4 ms) 30: [ RUN ] GetIrTest.AcceptsElectricField 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricField (3 ms) 30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (4 ms) 30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (3 ms) 30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (6 ms) 30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (3 ms) 30: [ RUN ] GetIrTest.RejectsImplicitSolventYes 30: [ OK ] GetIrTest.RejectsImplicitSolventYes (10 ms) 30: [ RUN ] GetIrTest.AcceptsMimic 30: 30: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsMimic (4 ms) 30: [----------] 14 tests from GetIrTest (86 ms total) 30: 30: [----------] 5 tests from SolvateTest 30: [ RUN ] SolvateTest.cs_box_Works 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 1x1x1 boxes 30: Solvent box contains 270 atoms in 90 residues 30: Removed 129 solvent atoms due to solvent-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 47 residues 30: Generated solvent containing 141 atoms in 47 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 30: 30: Output configuration contains 141 atoms in 47 residues 30: Volume : 1.331 (nm^3) 30: Density : 1056.36 (g/l) 30: Number of solvent molecules: 47 30: 30: [ OK ] SolvateTest.cs_box_Works (13 ms) 30: [ RUN ] SolvateTest.cs_cp_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 886 residues 30: Generated solvent containing 2658 atoms in 886 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 30: 30: Output configuration contains 2664 atoms in 888 residues 30: Volume : 27.2709 (nm^3) 30: Density : 974.777 (g/l) 30: Number of solvent molecules: 886 30: 30: [ OK ] SolvateTest.cs_cp_Works (109 ms) 30: [ RUN ] SolvateTest.cs_cp_p_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 886 residues 30: Generated solvent containing 2658 atoms in 886 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 30: 30: Output configuration contains 2664 atoms in 888 residues 30: Volume : 27.2709 (nm^3) 30: Density : 974.777 (g/l) 30: Number of solvent molecules: 886 30: 30: Processing topology 30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 30: [ OK ] SolvateTest.cs_cp_p_Works (115 ms) 30: [ RUN ] SolvateTest.shell_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 1902 solvent atoms more than 1.000000 nm from solute. 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 252 residues 30: Generated solvent containing 756 atoms in 252 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 30: 30: Output configuration contains 762 atoms in 254 residues 30: Volume : 27.2709 (nm^3) 30: Density : 279.3 (g/l) 30: Number of solvent molecules: 252 30: 30: [ OK ] SolvateTest.shell_Works (50 ms) 30: [ RUN ] SolvateTest.update_Topology_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 3x3x3 boxes 30: Solvent box contains 14952 atoms in 4984 residues 30: Removed 2787 solvent atoms due to solvent-solvent overlap 30: Removed 30 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 2 different molecule types: 30: HOH ( 3 atoms): 1876 residues 30: SOL ( 3 atoms): 2169 residues 30: Generated solvent containing 0 atoms in 0 residues 30: Writing generated configuration to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 30: 30: Output configuration contains 12141 atoms in 4047 residues 30: Volume : 125 (nm^3) 30: Density : 968.963 (g/l) 30: Number of solvent molecules: 4045 30: 30: Processing topology 30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 30: [ OK ] SolvateTest.update_Topology_Works (451 ms) 30: [----------] 5 tests from SolvateTest (738 ms total) 30: 30: [----------] 1 test from TopDirTests 30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 30: [----------] 1 test from TopDirTests (0 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 51 tests from 9 test cases ran. (2178 ms total) 30: [ PASSED ] 51 tests. 30/54 Test #30: GmxPreprocessTests .................. Passed 2.21 sec test 31 Start 31: Pdb2gmx1Test 31: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 31: Test timeout computed to be: 30 31: [==========] Running 24 tests from 1 test case. 31: [----------] Global test environment set-up. 31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (108 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (119 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (108 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (97 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (115 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (128 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (120 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (106 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (109 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (122 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (109 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (99 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (115 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (127 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (119 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (108 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (106 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (122 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (108 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (97 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (112 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (125 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (120 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (107 ms) 31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (2706 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 24 tests from 1 test case ran. (2706 ms total) 31: [ PASSED ] 24 tests. 31/54 Test #31: Pdb2gmx1Test ........................ Passed 2.74 sec test 32 Start 32: Pdb2gmx2Test 32: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 32: Test timeout computed to be: 30 32: [==========] Running 32 tests from 2 test cases. 32: [----------] Global test environment set-up. 32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (128 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (118 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (67 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (59 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Marked 37 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 37 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (110 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Marked 53 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 51 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (77 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Marked 36 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 36 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (66 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Marked 33 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 31 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (61 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (62 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (74 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (64 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (58 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Marked 37 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 37 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (63 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Marked 53 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 51 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (77 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Marked 36 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 36 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (66 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Marked 33 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 31 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (75 ms) 32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (1226 ms total) 32: 32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (71 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (153 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (134 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (127 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Marked 39 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 39 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (142 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Marked 57 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 55 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (169 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Marked 38 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 38 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (144 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Marked 35 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 33 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (126 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (128 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (148 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (84 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (66 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Marked 39 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 39 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (71 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Marked 57 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 55 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (86 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Marked 38 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 38 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (78 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Marked 35 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 33 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (69 ms) 32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (1796 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 32 tests from 2 test cases ran. (3022 ms total) 32: [ PASSED ] 32 tests. 32/54 Test #32: Pdb2gmx2Test ........................ Passed 3.06 sec test 33 Start 33: Pdb2gmx3Test 33: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 33: Test timeout computed to be: 30 33: [==========] Running 28 tests from 4 test cases. 33: [----------] Global test environment set-up. 33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 255, now 254 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 691 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 691 dihedrals, 51 impropers, 457 angles 33: 650 pairs, 254 bonds and 0 virtual sites 33: Total mass 1846.132 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (192 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 291, now 290 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 788 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 788 dihedrals, 72 impropers, 516 angles 33: 736 pairs, 290 bonds and 0 virtual sites 33: Total mass 2088.366 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (174 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 262, now 261 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 727 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 727 dihedrals, 56 impropers, 472 angles 33: 667 pairs, 261 bonds and 0 virtual sites 33: Total mass 1861.124 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (91 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 233, now 232 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 634 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 634 dihedrals, 48 impropers, 419 angles 33: 597 pairs, 232 bonds and 0 virtual sites 33: Total mass 1662.888 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (82 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 255, now 254 33: Marked 124 virtual sites 33: Added 16 dummy masses 33: Added 26 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 691 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 691 dihedrals, 51 impropers, 457 angles 33: 650 pairs, 254 bonds and 130 virtual sites 33: Total mass 1846.132 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (97 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 291, now 290 33: Marked 132 virtual sites 33: Added 10 dummy masses 33: Added 19 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 788 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 788 dihedrals, 72 impropers, 516 angles 33: 736 pairs, 290 bonds and 133 virtual sites 33: Total mass 2088.366 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (110 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 262, now 261 33: Marked 123 virtual sites 33: Added 22 dummy masses 33: Added 35 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 727 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 727 dihedrals, 56 impropers, 472 angles 33: 667 pairs, 261 bonds and 132 virtual sites 33: Total mass 1861.124 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (105 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 233, now 232 33: Marked 111 virtual sites 33: Added 18 dummy masses 33: Added 31 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 634 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 634 dihedrals, 48 impropers, 419 angles 33: 597 pairs, 232 bonds and 116 virtual sites 33: Total mass 1662.888 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (92 ms) 33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (943 ms total) 33: 33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 254, now 254 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 663 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 663 dihedrals, 48 impropers, 457 angles 33: 650 pairs, 254 bonds and 0 virtual sites 33: Total mass 1846.115 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (96 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 290, now 290 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 778 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 778 dihedrals, 49 impropers, 516 angles 33: 736 pairs, 290 bonds and 0 virtual sites 33: Total mass 2088.361 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus PHE-33: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (105 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 261, now 261 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 696 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 696 dihedrals, 39 impropers, 472 angles 33: 667 pairs, 261 bonds and 0 virtual sites 33: Total mass 1861.130 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Start terminus ALA-34: NH3+ 33: End terminus ALA-49: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (93 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 232, now 232 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 618 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 618 dihedrals, 38 impropers, 419 angles 33: 597 pairs, 232 bonds and 0 virtual sites 33: Total mass 1662.885 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Start terminus LYS-50: NH3+ 33: End terminus PRO-65: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (84 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 254, now 254 33: Marked 124 virtual sites 33: Added 16 dummy masses 33: Added 26 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 663 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 663 dihedrals, 48 impropers, 457 angles 33: 650 pairs, 254 bonds and 130 virtual sites 33: Total mass 1846.115 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (104 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 290, now 290 33: Marked 132 virtual sites 33: Added 10 dummy masses 33: Added 19 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 778 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 778 dihedrals, 49 impropers, 516 angles 33: 736 pairs, 290 bonds and 133 virtual sites 33: Total mass 2088.361 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus PHE-33: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (113 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 261, now 261 33: Marked 123 virtual sites 33: Added 22 dummy masses 33: Added 35 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 696 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 696 dihedrals, 39 impropers, 472 angles 33: 667 pairs, 261 bonds and 132 virtual sites 33: Total mass 1861.130 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Start terminus ALA-34: NH3+ 33: End terminus ALA-49: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (104 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 232, now 232 33: Marked 111 virtual sites 33: Added 18 dummy masses 33: Added 31 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 618 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 618 dihedrals, 38 impropers, 419 angles 33: 597 pairs, 232 bonds and 116 virtual sites 33: Total mass 1662.885 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Start terminus LYS-50: NH3+ 33: End terminus PRO-65: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (96 ms) 33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (795 ms total) 33: 33: [----------] 8 tests from ChainSep/Pdb2gmxTest 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 258, now 258 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 651 pairs 33: Before cleaning: 661 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 10 cmap torsion pairs 33: There are 661 dihedrals, 46 impropers, 463 angles 33: 648 pairs, 258 bonds and 0 virtual sites 33: Total mass 1882.146 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: 33: Merged chains into joint molecule definitions at 2 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Identified residue PHE6 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Start terminus PHE-6: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 258 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (105 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 50, now 50 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 123 pairs 33: Before cleaning: 123 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 123 dihedrals, 9 impropers, 88 angles 33: 123 pairs, 50 bonds and 0 virtual sites 33: Total mass 434.421 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 10 donors and 7 acceptors were found. 33: There are 7 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS8 33: NE223 33: MET12 SD55 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 125, now 125 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 317 pairs 33: Before cleaning: 322 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 5 cmap torsion pairs 33: There are 322 dihedrals, 19 impropers, 227 angles 33: 314 pairs, 125 bonds and 0 virtual sites 33: Total mass 846.083 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 258 atoms and 16 residues 33: Total mass in system 1882.146 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 4 28 33: 2 'B' 7 58 33: 3 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (28 atoms, 4 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 51 atoms 33: Chain time... 33: Processing chain 2 'B' (58 atoms, 7 residues) 33: Identified residue PHE6 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus PHE-6: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 7 residues with 124 atoms 33: Chain time... 33: Processing chain 3 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 51 atoms 4 residues 33: Including chain 2 in system: 124 atoms 7 residues 33: Including chain 3 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (70 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 258, now 258 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 651 pairs 33: Before cleaning: 661 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 10 cmap torsion pairs 33: There are 661 dihedrals, 46 impropers, 463 angles 33: 648 pairs, 258 bonds and 0 virtual sites 33: Total mass 1882.146 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: 33: Merged chains into joint molecule definitions at 2 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ILE-9: COO- 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 258 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (102 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 10 donors and 12 acceptors were found. 33: There are 13 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 33: SG9 33: HIS8 NE251 1.055 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 115, now 115 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 288 pairs 33: Before cleaning: 293 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 6 cmap torsion pairs 33: There are 293 dihedrals, 23 impropers, 203 angles 33: 285 pairs, 115 bonds and 0 virtual sites 33: Total mass 888.952 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 60, now 60 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 152 pairs 33: Before cleaning: 152 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 152 dihedrals, 5 impropers, 112 angles 33: 152 pairs, 60 bonds and 0 virtual sites 33: Total mass 391.552 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 258 atoms and 16 residues 33: Total mass in system 1882.146 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 8 61 33: 2 'B' 3 25 33: 3 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (61 atoms, 8 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ILE-9: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 8 residues with 114 atoms 33: Chain time... 33: Processing chain 2 'B' (25 atoms, 3 residues) 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 61 atoms 33: Chain time... 33: Processing chain 3 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 114 atoms 8 residues 33: Including chain 2 in system: 61 atoms 3 residues 33: Including chain 3 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (72 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 260, now 260 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 650 pairs 33: Before cleaning: 660 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 8 cmap torsion pairs 33: There are 660 dihedrals, 45 impropers, 466 angles 33: 647 pairs, 260 bonds and 0 virtual sites 33: Total mass 1900.162 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: 33: Merged chains into joint molecule definitions at 3 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Identified residue PHE6 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Start terminus PHE-6: NH3+ 33: End terminus ILE-9: COO- 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 261 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (104 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 50, now 50 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 123 pairs 33: Before cleaning: 123 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 123 dihedrals, 9 impropers, 88 angles 33: 123 pairs, 50 bonds and 0 virtual sites 33: Total mass 434.421 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 6 donors and 4 acceptors were found. 33: There are 3 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 67, now 67 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 164 pairs 33: Before cleaning: 169 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 169 dihedrals, 13 impropers, 118 angles 33: 161 pairs, 67 bonds and 0 virtual sites 33: Total mass 472.547 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 60, now 60 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 152 pairs 33: Before cleaning: 152 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 152 dihedrals, 5 impropers, 112 angles 33: 152 pairs, 60 bonds and 0 virtual sites 33: Total mass 391.552 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 261 atoms and 16 residues 33: Total mass in system 1900.162 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: WARNING: Chain identifier 'B' is used in two non-sequential blocks. 33: They will be treated as separate chains unless you reorder your file. 33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 4 28 33: 2 'B' 4 33 33: 3 'B' 3 25 33: 4 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (28 atoms, 4 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 51 atoms 33: Chain time... 33: Processing chain 2 'B' (33 atoms, 4 residues) 33: Identified residue PHE6 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Start terminus PHE-6: NH3+ 33: End terminus ILE-9: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 66 atoms 33: Chain time... 33: Processing chain 3 'B' (25 atoms, 3 residues) 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 61 atoms 33: Chain time... 33: Processing chain 4 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 51 atoms 4 residues 33: Including chain 2 in system: 66 atoms 4 residues 33: Including chain 3 in system: 61 atoms 3 residues 33: Including chain 4 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (69 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 256, now 256 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 652 pairs 33: Before cleaning: 662 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 12 cmap torsion pairs 33: There are 662 dihedrals, 47 impropers, 460 angles 33: 649 pairs, 256 bonds and 0 virtual sites 33: Total mass 1864.131 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: 33: Merged chains into joint molecule definitions at 1 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (100 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 14 donors and 15 acceptors were found. 33: There are 20 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 173, now 173 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 441 pairs 33: Before cleaning: 446 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 9 cmap torsion pairs 33: There are 446 dihedrals, 29 impropers, 312 angles 33: 438 pairs, 173 bonds and 0 virtual sites 33: Total mass 1262.488 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 255 atoms and 16 residues 33: Total mass in system 1864.131 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 11 86 33: 2 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (86 atoms, 11 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 11 residues with 172 atoms 33: Chain time... 33: Processing chain 2 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 172 atoms 11 residues 33: Including chain 2 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (76 ms) 33: [----------] 8 tests from ChainSep/Pdb2gmxTest (698 ms total) 33: 33: [----------] 4 tests from ChainChanges/Pdb2gmxTest 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (48 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (49 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (48 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/reproducible-path/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (48 ms) 33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (193 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 28 tests from 4 test cases ran. (2629 ms total) 33: [ PASSED ] 28 tests. 33/54 Test #33: Pdb2gmx3Test ........................ Passed 2.67 sec test 34 Start 34: CorrelationsTest 34: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 3 test cases. 34: [----------] Global test environment set-up. 34: [----------] 10 tests from AutocorrTest 34: [ RUN ] AutocorrTest.EacNormal 34: [ OK ] AutocorrTest.EacNormal (116 ms) 34: [ RUN ] AutocorrTest.EacNoNormalize 34: [ OK ] AutocorrTest.EacNoNormalize (75 ms) 34: [ RUN ] AutocorrTest.EacCos 34: [ OK ] AutocorrTest.EacCos (139 ms) 34: [ RUN ] AutocorrTest.EacVector 34: [ OK ] AutocorrTest.EacVector (216 ms) 34: [ RUN ] AutocorrTest.EacRcross 34: [ OK ] AutocorrTest.EacRcross (1 ms) 34: [ RUN ] AutocorrTest.EacP0 34: [ OK ] AutocorrTest.EacP0 (223 ms) 34: [ RUN ] AutocorrTest.EacP1 34: [ OK ] AutocorrTest.EacP1 (221 ms) 34: [ RUN ] AutocorrTest.EacP2 34: [ OK ] AutocorrTest.EacP2 (435 ms) 34: [ RUN ] AutocorrTest.EacP3 34: [ OK ] AutocorrTest.EacP3 (4 ms) 34: [ RUN ] AutocorrTest.EacP4 34: [ OK ] AutocorrTest.EacP4 (215 ms) 34: [----------] 10 tests from AutocorrTest (1648 ms total) 34: 34: [----------] 1 test from ManyAutocorrelationTest 34: [ RUN ] ManyAutocorrelationTest.Empty 34: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 34: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 34: 34: [----------] 10 tests from ExpfitTest 34: [ RUN ] ExpfitTest.EffnEXP1 34: [ OK ] ExpfitTest.EffnEXP1 (1 ms) 34: [ RUN ] ExpfitTest.EffnEXP2 34: [ OK ] ExpfitTest.EffnEXP2 (1 ms) 34: [ RUN ] ExpfitTest.EffnEXPEXP 34: [ OK ] ExpfitTest.EffnEXPEXP (2 ms) 34: [ RUN ] ExpfitTest.EffnEXP5 34: [ OK ] ExpfitTest.EffnEXP5 (16 ms) 34: [ RUN ] ExpfitTest.EffnEXP7 34: [ OK ] ExpfitTest.EffnEXP7 (13 ms) 34: [ RUN ] ExpfitTest.EffnEXP9 34: [ OK ] ExpfitTest.EffnEXP9 (27 ms) 34: [ RUN ] ExpfitTest.EffnERF 34: [ OK ] ExpfitTest.EffnERF (3 ms) 34: [ RUN ] ExpfitTest.EffnERREST 34: [ OK ] ExpfitTest.EffnERREST (1 ms) 34: [ RUN ] ExpfitTest.EffnVAC 34: [ OK ] ExpfitTest.EffnVAC (7 ms) 34: [ RUN ] ExpfitTest.EffnPRES 34: [ OK ] ExpfitTest.EffnPRES (19 ms) 34: [----------] 10 tests from ExpfitTest (90 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 3 test cases ran. (1755 ms total) 34: [ PASSED ] 21 tests. 34/54 Test #34: CorrelationsTest .................... Passed 1.79 sec test 35 Start 35: AnalysisDataUnitTests 35: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 35: Test timeout computed to be: 30 35: [==========] Running 69 tests from 14 test cases. 35: [----------] Global test environment set-up. 35: [----------] 3 tests from AnalysisDataInitializationTest 35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 35: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/0 (3 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (9 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/1 (12 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (5 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/2 (8 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/3 (8 ms total) 35: 35: [----------] 4 tests from AnalysisArrayDataTest 35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (5 ms) 35: [ RUN ] AnalysisArrayDataTest.StorageWorks 35: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 35: [----------] 4 tests from AnalysisArrayDataTest (5 ms total) 35: 35: [----------] 6 tests from AverageModuleTest 35: [ RUN ] AverageModuleTest.BasicTest 35: [ OK ] AverageModuleTest.BasicTest (1 ms) 35: [ RUN ] AverageModuleTest.HandlesMultipointData 35: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (1 ms) 35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms) 35: [ RUN ] AverageModuleTest.CanCustomizeXAxis 35: [ OK ] AverageModuleTest.CanCustomizeXAxis (1 ms) 35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 35: [----------] 6 tests from AverageModuleTest (9 ms total) 35: 35: [----------] 2 tests from FrameAverageModuleTest 35: [ RUN ] FrameAverageModuleTest.BasicTest 35: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 35: [----------] 2 tests from FrameAverageModuleTest (1 ms total) 35: 35: [----------] 7 tests from AnalysisHistogramSettingsTest 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 35: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 35: 35: [----------] 2 tests from SimpleHistogramModuleTest 35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (5 ms) 35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [----------] 2 tests from SimpleHistogramModuleTest (7 ms total) 35: 35: [----------] 3 tests from WeightedHistogramModuleTest 35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (5 ms) 35: [----------] 3 tests from WeightedHistogramModuleTest (7 ms total) 35: 35: [----------] 3 tests from BinAverageModuleTest 35: [ RUN ] BinAverageModuleTest.ComputesCorrectly 35: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 35: [----------] 3 tests from BinAverageModuleTest (2 ms total) 35: 35: [----------] 4 tests from AbstractAverageHistogramTest 35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (6 ms) 35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) 35: [----------] 4 tests from AbstractAverageHistogramTest (9 ms total) 35: 35: [----------] 3 tests from LifetimeModuleTest 35: [ RUN ] LifetimeModuleTest.BasicTest 35: [ OK ] LifetimeModuleTest.BasicTest (4 ms) 35: [ RUN ] LifetimeModuleTest.CumulativeTest 35: [ OK ] LifetimeModuleTest.CumulativeTest (1 ms) 35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (1 ms) 35: [----------] 3 tests from LifetimeModuleTest (6 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 69 tests from 14 test cases ran. (77 ms total) 35: [ PASSED ] 69 tests. 35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.12 sec test 36 Start 36: CoordinateIOTests 36: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 36: Test timeout computed to be: 30 36: [==========] Running 64 tests from 19 test cases. 36: [----------] Global test environment set-up. 36: [----------] 1 test from OutputSelectorDeathTest 36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (23 ms) 36: [----------] 1 test from OutputSelectorDeathTest (23 ms total) 36: 36: [----------] 5 tests from TrajectoryFrameWriterTest 36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (4 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (12 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (5 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (17 ms) 36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 36: [----------] 5 tests from TrajectoryFrameWriterTest (38 ms total) 36: 36: [----------] 5 tests from OutputAdapterContainer 36: [ RUN ] OutputAdapterContainer.MakeEmpty 36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 36: [ RUN ] OutputAdapterContainer.AddAdapter 36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.RejectBadAdapter 36: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 36: [----------] 5 tests from OutputAdapterContainer (0 ms total) 36: 36: [----------] 5 tests from FlagTest 36: [ RUN ] FlagTest.CanSetSimpleFlag 36: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 36: [ RUN ] FlagTest.CanAddNewBox 36: [ OK ] FlagTest.CanAddNewBox (0 ms) 36: [ RUN ] FlagTest.SetsImplicitPrecisionChange 36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 36: [ RUN ] FlagTest.SetsImplicitStartTimeChange 36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 36: [ RUN ] FlagTest.SetsImplicitTimeStepChange 36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 36: [----------] 5 tests from FlagTest (0 ms total) 36: 36: [----------] 5 tests from SetAtomsTest 36: [ RUN ] SetAtomsTest.RemovesExistingAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.RemovesExistingAtoms (13 ms) 36: [ RUN ] SetAtomsTest.AddsNewAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.AddsNewAtoms (4 ms) 36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (12 ms) 36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (4 ms) 36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (13 ms) 36: [----------] 5 tests from SetAtomsTest (46 ms total) 36: 36: [----------] 2 tests from SetBothTimeTest 36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 36: [----------] 2 tests from SetBothTimeTest (0 ms total) 36: 36: [----------] 2 tests from SetStartTimeTest 36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 36: [ RUN ] SetStartTimeTest.WorksWithZeroStart 36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 36: [----------] 2 tests from SetStartTimeTest (0 ms total) 36: 36: [----------] 1 test from SetTimeStepTest 36: [ RUN ] SetTimeStepTest.SetTimeStepWorks 36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 36: [----------] 1 test from SetTimeStepTest (0 ms total) 36: 36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (12 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (5 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (12 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (4 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (12 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (5 ms) 36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (50 ms total) 36: 36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (8 ms) 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (12 ms) 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (4 ms) 36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (24 ms total) 36: 36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (1 ms) 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total) 36: 36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (24 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (17 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (17 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (16 ms) 36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (74 ms total) 36: 36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (5 ms) 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (12 ms) 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (4 ms) 36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (21 ms total) 36: 36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (1 ms) 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total) 36: 36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (12 ms) 36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (12 ms) 36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (24 ms total) 36: 36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (1 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total) 36: 36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (4 ms) 36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (12 ms) 36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (16 ms total) 36: 36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (1 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total) 36: 36: [----------] 4 tests from ModuleSupported/NoOptionalOutput 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (4 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (12 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (4 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (13 ms) 36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (33 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 64 tests from 19 test cases ran. (353 ms total) 36: [ PASSED ] 64 tests. 36/54 Test #36: CoordinateIOTests ................... Passed 0.40 sec test 37 Start 37: TrajectoryAnalysisUnitTests 37: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 37: Test timeout computed to be: 30 37: [==========] Running 82 tests from 16 test cases. 37: [----------] Global test environment set-up. 37: [----------] 5 tests from ClustsizeTest 37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 37: There is one group in the index 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 24 37: cmid: 2, cmax: 4, max_size: 6 37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) 37: [ RUN ] ClustsizeTest.NoMolShortCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 37: There is one group in the index 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 24 37: cmid: 1, cmax: 6, max_size: 6 37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (6 ms) 37: [ RUN ] ClustsizeTest.MolDefaultCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 2, cmax: 4, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (1 ms) 37: [ RUN ] ClustsizeTest.MolShortCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 1, cmax: 6, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) 37: [ RUN ] ClustsizeTest.MolCSize 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 2, cmax: 4, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolCSize (6 ms) 37: [----------] 5 tests from ClustsizeTest (16 ms total) 37: 37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 37: Reading frames from gro file 'Test system', 8 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (8 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 37: Reading frames from gro file 'Test system', 8 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (15 ms total) 37: 37: [----------] 11 tests from AngleModuleTest 37: [ RUN ] AngleModuleTest.ComputesSimpleAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesSimpleAngles (8 ms) 37: [ RUN ] AngleModuleTest.ComputesDihedrals 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesDihedrals (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (7 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (7 ms) 37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (4 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 37: Reading frames from gro file 'Test system for different angles', 33 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesMultipleAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesMultipleAngles (4 ms) 37: [ RUN ] AngleModuleTest.HandlesDynamicSelections 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesDynamicSelections (3 ms) 37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (3 ms) 37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (3 ms) 37: [----------] 11 tests from AngleModuleTest (48 ms total) 37: 37: [----------] 4 tests from ConvertTrjModuleTest 37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (11 ms) 37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (12 ms) 37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) 37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 37: [----------] 4 tests from ConvertTrjModuleTest (25 ms total) 37: 37: [----------] 3 tests from DistanceModuleTest 37: [ RUN ] DistanceModuleTest.ComputesDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2: 37: Number of samples: 5 37: Average distance: 1.43246 nm 37: Standard deviation: 0.96700 nm 37: [ OK ] DistanceModuleTest.ComputesDistances (5 ms) 37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2: 37: Number of samples: 5 37: Average distance: 1.43246 nm 37: Standard deviation: 0.96700 nm 37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 37: Number of samples: 4 37: Average distance: 1.81066 nm 37: Standard deviation: 0.79289 nm 37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (4 ms) 37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2 and res_cog x < 2.8: 37: Number of samples: 3 37: Average distance: 1.72076 nm 37: Standard deviation: 1.24839 nm 37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (3 ms) 37: [----------] 3 tests from DistanceModuleTest (13 ms total) 37: 37: [----------] 2 tests from ExtractClusterModuleTest 37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 37: trr version: GMX_trn_file (single precision) 37: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 37: Analyzed 26 frames, last time 0.050 37: There are 8 clusters containing 26 structures, highest framenr is 25 37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (2 ms) 37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 37: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 37: Analyzed 26 frames, last time 0.050 37: There are 8 clusters containing 26 structures, highest framenr is 25 37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (2 ms) 37: [----------] 2 tests from ExtractClusterModuleTest (4 ms total) 37: 37: [----------] 2 tests from FreeVolumeModuleTest 37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for 40 particles. These were set to zero. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: cutoff = 0.18 nm 37: probe_radius = 0 nm 37: seed = 13 37: ninsert = 1000 probes per nm^3 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 37: van der Spoel and Luciano T. Costa 37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Free volume 38.02 +/- 0.00 % 37: Total volume 68.92 +/- 0.00 nm^3 37: Number of molecules 340 total mass 63491.38 Dalton 37: Average molar mass: 186.74 Dalton 37: Density rho: 1529.71 +/- 0.00 nm^3 37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 37: Fractional free volume 0.194 +/- 0.000 37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (112 ms) 37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: cutoff = 0.18 nm 37: probe_radius = 0 nm 37: seed = 17 37: ninsert = 1000 probes per nm^3 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 37: van der Spoel and Luciano T. Costa 37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Free volume 38.48 +/- 0.00 % 37: Total volume 68.92 +/- 0.00 nm^3 37: Number of molecules 340 total mass 63491.38 Dalton 37: Average molar mass: 186.74 Dalton 37: Density rho: 1529.71 +/- 0.00 nm^3 37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 37: Fractional free volume 0.200 +/- 0.000 37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (114 ms) 37: [----------] 2 tests from FreeVolumeModuleTest (226 ms total) 37: 37: [----------] 9 tests from PairDistanceModuleTest 37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (4 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (2 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (4 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (4 ms) 37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (3 ms) 37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (3 ms) 37: [----------] 9 tests from PairDistanceModuleTest (29 ms total) 37: 37: [----------] 5 tests from RdfModuleTest 37: [ RUN ] RdfModuleTest.BasicTest 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.BasicTest (28 ms) 37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (18 ms) 37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (29 ms) 37: [ RUN ] RdfModuleTest.CalculatesSurf 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.CalculatesSurf (17 ms) 37: [ RUN ] RdfModuleTest.CalculatesXY 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.CalculatesXY (32 ms) 37: [----------] 5 tests from RdfModuleTest (124 ms total) 37: 37: [----------] 5 tests from SasaModuleTest 37: [ RUN ] SasaModuleTest.BasicTest 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.BasicTest (15 ms) 37: [ RUN ] SasaModuleTest.HandlesSelectedResidues 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesSelectedResidues (9 ms) 37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (9 ms) 37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (13 ms) 37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (11 ms) 37: [----------] 5 tests from SasaModuleTest (58 ms total) 37: 37: [----------] 8 tests from SelectModuleTest 37: [ RUN ] SelectModuleTest.BasicTest 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.BasicTest (5 ms) 37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (5 ms) 37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (5 ms) 37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (5 ms) 37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (5 ms) 37: [ RUN ] SelectModuleTest.NormalizesSizes 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.NormalizesSizes (3 ms) 37: [ RUN ] SelectModuleTest.WritesResidueNumbers 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.WritesResidueNumbers (3 ms) 37: [ RUN ] SelectModuleTest.WritesResidueIndices 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.WritesResidueIndices (4 ms) 37: [----------] 8 tests from SelectModuleTest (35 ms total) 37: 37: [----------] 10 tests from SurfaceAreaTest 37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (1 ms) 37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (1 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints12 37: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints32 37: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints42 37: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints122 37: [ OK ] SurfaceAreaTest.SurfacePoints122 (2 ms) 37: [ RUN ] SurfaceAreaTest.Computes100Points 37: [ OK ] SurfaceAreaTest.Computes100Points (1 ms) 37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (2 ms) 37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (4 ms) 37: [----------] 10 tests from SurfaceAreaTest (12 ms total) 37: 37: [----------] 4 tests from TopologyInformation 37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 37: [ RUN ] TopologyInformation.WorksWithGroFile 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TopologyInformation.WorksWithGroFile (5 ms) 37: [ RUN ] TopologyInformation.WorksWithPdbFile 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TopologyInformation.WorksWithPdbFile (4 ms) 37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 37: 37: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1073759265 37: Generated 330891 of the 330891 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 330891 of the 330891 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 37: 37: NOTE 2 [file lysozyme.top, line 1465]: 37: System has non-zero total charge: 2.000000 37: Total charge should normally be an integer. See 37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 37: for discussion on how close it should be to an integer. 37: 37: 37: 37: Number of degrees of freedom in T-Coupling group rest is 465.00 37: 37: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 37: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 37: Analysing residue names: 37: There are: 10 Protein residues 37: Analysing Protein... 37: This run will generate roughly 0 Mb of data 37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (669 ms) 37: [----------] 4 tests from TopologyInformation (678 ms total) 37: 37: [----------] 4 tests from TrajectoryModuleTest 37: [ RUN ] TrajectoryModuleTest.BasicTest 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.BasicTest (4 ms) 37: [ RUN ] TrajectoryModuleTest.PlotsXOnly 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.PlotsXOnly (4 ms) 37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (3 ms) 37: [ RUN ] TrajectoryModuleTest.HandlesNoForces 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.HandlesNoForces (3 ms) 37: [----------] 4 tests from TrajectoryModuleTest (14 ms total) 37: 37: [----------] 5 tests from UnionFinderTest 37: [ RUN ] UnionFinderTest.WorksEmpty 37: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 37: [ RUN ] UnionFinderTest.BasicMerges 37: [ OK ] UnionFinderTest.BasicMerges (0 ms) 37: [ RUN ] UnionFinderTest.LargerMerges 37: [ OK ] UnionFinderTest.LargerMerges (0 ms) 37: [ RUN ] UnionFinderTest.LongRightMerge 37: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 37: [ RUN ] UnionFinderTest.LongLeftMerge 37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 37: [----------] 5 tests from UnionFinderTest (0 ms total) 37: 37: [----------] 1 test from MappedUnionFinderTest 37: [ RUN ] MappedUnionFinderTest.BasicMerges 37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 37: [----------] 1 test from MappedUnionFinderTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 82 tests from 16 test cases ran. (1298 ms total) 37: [ PASSED ] 82 tests. 37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 1.34 sec test 38 Start 38: EnergyAnalysisUnitTests 38: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 38: Test timeout computed to be: 30 38: [==========] Running 7 tests from 4 test cases. 38: [----------] Global test environment set-up. 38: [----------] 1 test from DhdlTest 38: [ RUN ] DhdlTest.ExtractDhdl 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 38: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 38: Note: file tpx version 110, software tpx version 119 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 38: 38: 38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 38: [ OK ] DhdlTest.ExtractDhdl (18 ms) 38: [----------] 1 test from DhdlTest (18 ms total) 38: 38: [----------] 1 test from OriresTest 38: [ RUN ] OriresTest.ExtractOrires 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 38: Reading file /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 38: Note: file tpx version 111, software tpx version 119 38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 38: End your selection with 0 38: Selecting all 7 orientation restraints 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 38: [ OK ] OriresTest.ExtractOrires (28 ms) 38: [----------] 1 test from OriresTest (28 ms total) 38: 38: [----------] 3 tests from EnergyTest 38: [ RUN ] EnergyTest.ExtractEnergy 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 38: [ OK ] EnergyTest.ExtractEnergy (2 ms) 38: [ RUN ] EnergyTest.ExtractEnergyByNumber 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 38: Pres. DC -268.49 3 8.52175 13.2804 (bar) 38: [ OK ] EnergyTest.ExtractEnergyByNumber (2 ms) 38: [ RUN ] EnergyTest.ExtractEnergyMixed 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: [ OK ] EnergyTest.ExtractEnergyMixed (11 ms) 38: [----------] 3 tests from EnergyTest (16 ms total) 38: 38: [----------] 2 tests from ViscosityTest 38: [ RUN ] ViscosityTest.EinsteinViscosity 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Pres-XX 20.2092 65 717.193 185.978 (bar) 38: Pres-XY -47.7351 39 372.522 207.456 (bar) 38: Pres-XZ 11.477 31 379.79 6.80818 (bar) 38: Pres-YX -47.7106 39 372.525 207.5 (bar) 38: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 38: Pres-YZ -41.3534 45 401.216 114.663 (bar) 38: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 38: Pres-ZY -41.3119 45 401.196 114.743 (bar) 38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 38: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: [ OK ] ViscosityTest.EinsteinViscosity (278 ms) 38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 38: Opened /build/reproducible-path/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Pres-XX 20.2092 65 717.193 185.978 (bar) 38: Pres-XY -47.7351 39 372.522 207.456 (bar) 38: Pres-XZ 11.477 31 379.79 6.80818 (bar) 38: Pres-YX -47.7106 39 372.525 207.5 (bar) 38: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 38: Pres-YZ -41.3534 45 401.216 114.663 (bar) 38: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 38: Pres-ZY -41.3119 45 401.196 114.743 (bar) 38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 38: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (260 ms) 38: [----------] 2 tests from ViscosityTest (538 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 7 tests from 4 test cases ran. (600 ms total) 38: [ PASSED ] 7 tests. 38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 0.65 sec test 39 Start 39: ToolUnitTests 39: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 39: Test timeout computed to be: 30 39: [==========] Running 18 tests from 4 test cases. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from DumpTest 39: 39: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: For a correct single-point energy evaluation with nsteps = 0, use 39: continuation = yes to avoid constraining the input coordinates. 39: 39: Setting the LD random seed to -538017953 39: Generated 330891 of the 330891 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 330891 of the 330891 1-4 parameter combinations 39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 39: 39: NOTE 2 [file lysozyme.top, line 1465]: 39: System has non-zero total charge: 2.000000 39: Total charge should normally be an integer. See 39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 39: for discussion on how close it should be to an integer. 39: 39: 39: 39: Number of degrees of freedom in T-Coupling group rest is 465.00 39: 39: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: NVE simulation with an initial temperature of zero: will use a Verlet 39: buffer of 10%. Check your energy drift! 39: 39: 39: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: You are using a plain Coulomb cut-off, which might produce artifacts. 39: You might want to consider using PME electrostatics. 39: 39: 39: 39: There were 4 notes 39: Analysing residue names: 39: There are: 10 Protein residues 39: Analysing Protein... 39: This run will generate roughly 0 Mb of data 39: [ RUN ] DumpTest.WorksWithTpr 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 39: inputrec: 39: integrator = md 39: tinit = 0 39: dt = 0.001 39: nsteps = 0 39: init-step = 0 39: simulation-part = 1 39: comm-mode = Linear 39: nstcomm = 100 39: bd-fric = 0 39: ld-seed = -538017953 39: emtol = 10 39: emstep = 0.01 39: niter = 20 39: fcstep = 0 39: nstcgsteep = 1000 39: nbfgscorr = 10 39: rtpi = 0.05 39: nstxout = 0 39: nstvout = 0 39: nstfout = 0 39: nstlog = 1000 39: nstcalcenergy = 100 39: nstenergy = 1000 39: nstxout-compressed = 0 39: compressed-x-precision = 1000 39: cutoff-scheme = Verlet 39: nstlist = 10 39: pbc = xyz 39: periodic-molecules = false 39: verlet-buffer-tolerance = -1 39: rlist = 1.1 39: coulombtype = Cut-off 39: coulomb-modifier = Potential-shift 39: rcoulomb-switch = 0 39: rcoulomb = 1 39: epsilon-r = 1 39: epsilon-rf = inf 39: vdw-type = Cut-off 39: vdw-modifier = Potential-shift 39: rvdw-switch = 0 39: rvdw = 1 39: DispCorr = No 39: table-extension = 1 39: fourierspacing = 0.12 39: fourier-nx = 0 39: fourier-ny = 0 39: fourier-nz = 0 39: pme-order = 4 39: ewald-rtol = 1e-05 39: ewald-rtol-lj = 0.001 39: lj-pme-comb-rule = Geometric 39: ewald-geometry = 0 39: epsilon-surface = 0 39: tcoupl = No 39: nsttcouple = -1 39: nh-chain-length = 0 39: print-nose-hoover-chain-variables = false 39: pcoupl = No 39: pcoupltype = Isotropic 39: nstpcouple = -1 39: tau-p = 1 39: compressibility (3x3): 39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p (3x3): 39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: refcoord-scaling = No 39: posres-com (3): 39: posres-com[0]= 0.00000e+00 39: posres-com[1]= 0.00000e+00 39: posres-com[2]= 0.00000e+00 39: posres-comB (3): 39: posres-comB[0]= 0.00000e+00 39: posres-comB[1]= 0.00000e+00 39: posres-comB[2]= 0.00000e+00 39: QMMM = false 39: QMconstraints = 0 39: QMMMscheme = 0 39: MMChargeScaleFactor = 1 39: qm-opts: 39: ngQM = 0 39: constraint-algorithm = Lincs 39: continuation = false 39: Shake-SOR = false 39: shake-tol = 0.0001 39: lincs-order = 4 39: lincs-iter = 1 39: lincs-warnangle = 30 39: nwall = 0 39: wall-type = 9-3 39: wall-r-linpot = -1 39: wall-atomtype[0] = -1 39: wall-atomtype[1] = -1 39: wall-density[0] = 0 39: wall-density[1] = 0 39: wall-ewald-zfac = 3 39: pull = false 39: awh = false 39: rotation = false 39: interactiveMD = false 39: disre = No 39: disre-weighting = Conservative 39: disre-mixed = false 39: dr-fc = 1000 39: dr-tau = 0 39: nstdisreout = 100 39: orire-fc = 0 39: orire-tau = 0 39: nstorireout = 100 39: free-energy = no 39: cos-acceleration = 0 39: deform (3x3): 39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: simulated-tempering = false 39: swapcoords = no 39: userint1 = 0 39: userint2 = 0 39: userint3 = 0 39: userint4 = 0 39: userreal1 = 0 39: userreal2 = 0 39: userreal3 = 0 39: userreal4 = 0 39: applied-forces: 39: electric-field: 39: x: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: y: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: z: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: density-guided-simulation: 39: active = false 39: group = protein 39: similarity-measure = inner-product 39: atom-spreading-weight = unity 39: force-constant = 1e+09 39: gaussian-transform-spreading-width = 0.2 39: gaussian-transform-spreading-range-in-multiples-of-width = 4 39: reference-density-filename = reference.mrc 39: nst = 1 39: normalize-densities = true 39: adaptive-force-scaling = false 39: adaptive-force-scaling-time-constant = 4 39: grpopts: 39: nrdf: 465 39: ref-t: 0 39: tau-t: 0 39: annealing: No 39: annealing-npoints: 0 39: acc: 0 0 0 39: nfreeze: N N N 39: energygrp-flags[ 0]: 0 39: header: 39: bIr = present 39: bBox = present 39: bTop = present 39: bX = present 39: bV = present 39: bF = not present 39: natoms = 156 39: lambda = 0.000000e+00 39: buffer size = 70122 39: topology: 39: name="First 10 residues from 1AKI" 39: #atoms = 156 39: #molblock = 1 39: molblock (0): 39: moltype = 0 "Protein_chain_B" 39: #molecules = 1 39: #posres_xA = 0 39: #posres_xB = 0 39: bIntermolecularInteractions = false 39: ffparams: 39: atnr=10 39: ntypes=212 39: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 39: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 39: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 39: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 39: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 39: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 39: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 39: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 39: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 39: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 39: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 39: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 39: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 39: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 39: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 39: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 39: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 39: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 39: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 39: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 39: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 39: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 39: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 39: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 39: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 39: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05 39: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 39: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 39: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 39: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 39: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 39: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 39: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 39: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 39: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06 39: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 39: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 39: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 39: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 39: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 39: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 39: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 39: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 39: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06 39: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 39: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 39: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 39: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 39: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 39: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 39: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 39: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 39: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 39: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08 39: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 39: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 39: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 39: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 39: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 39: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 39: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 39: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 39: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08 39: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 39: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 39: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 39: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 39: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 39: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 39: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 39: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 39: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 39: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05 39: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 39: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 39: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 39: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 39: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 39: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 39: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 39: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 39: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 39: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 39: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 39: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 39: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 39: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 39: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 39: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 39: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 39: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 39: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 39: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 39: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 39: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 39: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 39: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 39: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 39: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 39: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 39: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 39: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 39: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 39: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 39: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 39: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 39: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 39: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 39: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 39: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 39: reppow = 12 39: fudgeQQ = 0.5 39: cmap 39: atomtypes: 39: atomtype[ 0]={atomnumber= 7} 39: atomtype[ 1]={atomnumber= 1} 39: atomtype[ 2]={atomnumber= 6} 39: atomtype[ 3]={atomnumber= 1} 39: atomtype[ 4]={atomnumber= 6} 39: atomtype[ 5]={atomnumber= 8} 39: atomtype[ 6]={atomnumber= 6} 39: atomtype[ 7]={atomnumber= 1} 39: atomtype[ 8]={atomnumber= 6} 39: atomtype[ 9]={atomnumber= 16} 39: moltype (0): 39: name="Protein_chain_B" 39: atoms: 39: atom (156): 39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 39: atom (156): 39: atom[0]={name="N"} 39: atom[1]={name="H1"} 39: atom[2]={name="H2"} 39: atom[3]={name="H3"} 39: atom[4]={name="CA"} 39: atom[5]={name="HA"} 39: atom[6]={name="CB"} 39: atom[7]={name="HB1"} 39: atom[8]={name="HB2"} 39: atom[9]={name="CG"} 39: atom[10]={name="HG1"} 39: atom[11]={name="HG2"} 39: atom[12]={name="CD"} 39: atom[13]={name="HD1"} 39: atom[14]={name="HD2"} 39: atom[15]={name="CE"} 39: atom[16]={name="HE1"} 39: atom[17]={name="HE2"} 39: atom[18]={name="NZ"} 39: atom[19]={name="HZ1"} 39: atom[20]={name="HZ2"} 39: atom[21]={name="HZ3"} 39: atom[22]={name="C"} 39: atom[23]={name="O"} 39: atom[24]={name="N"} 39: atom[25]={name="H"} 39: atom[26]={name="CA"} 39: atom[27]={name="HA"} 39: atom[28]={name="CB"} 39: atom[29]={name="HB"} 39: atom[30]={name="CG1"} 39: atom[31]={name="HG11"} 39: atom[32]={name="HG12"} 39: atom[33]={name="HG13"} 39: atom[34]={name="CG2"} 39: atom[35]={name="HG21"} 39: atom[36]={name="HG22"} 39: atom[37]={name="HG23"} 39: atom[38]={name="C"} 39: atom[39]={name="O"} 39: atom[40]={name="N"} 39: atom[41]={name="H"} 39: atom[42]={name="CA"} 39: atom[43]={name="HA"} 39: atom[44]={name="CB"} 39: atom[45]={name="HB1"} 39: atom[46]={name="HB2"} 39: atom[47]={name="CG"} 39: atom[48]={name="CD1"} 39: atom[49]={name="HD1"} 39: atom[50]={name="CD2"} 39: atom[51]={name="HD2"} 39: atom[52]={name="CE1"} 39: atom[53]={name="HE1"} 39: atom[54]={name="CE2"} 39: atom[55]={name="HE2"} 39: atom[56]={name="CZ"} 39: atom[57]={name="HZ"} 39: atom[58]={name="C"} 39: atom[59]={name="O"} 39: atom[60]={name="N"} 39: atom[61]={name="H"} 39: atom[62]={name="CA"} 39: atom[63]={name="HA1"} 39: atom[64]={name="HA2"} 39: atom[65]={name="C"} 39: atom[66]={name="O"} 39: atom[67]={name="N"} 39: atom[68]={name="H"} 39: atom[69]={name="CA"} 39: atom[70]={name="HA"} 39: atom[71]={name="CB"} 39: atom[72]={name="HB1"} 39: atom[73]={name="HB2"} 39: atom[74]={name="CG"} 39: atom[75]={name="HG1"} 39: atom[76]={name="HG2"} 39: atom[77]={name="CD"} 39: atom[78]={name="HD1"} 39: atom[79]={name="HD2"} 39: atom[80]={name="NE"} 39: atom[81]={name="HE"} 39: atom[82]={name="CZ"} 39: atom[83]={name="NH1"} 39: atom[84]={name="HH11"} 39: atom[85]={name="HH12"} 39: atom[86]={name="NH2"} 39: atom[87]={name="HH21"} 39: atom[88]={name="HH22"} 39: atom[89]={name="C"} 39: atom[90]={name="O"} 39: atom[91]={name="N"} 39: atom[92]={name="H"} 39: atom[93]={name="CA"} 39: atom[94]={name="HA"} 39: atom[95]={name="CB"} 39: atom[96]={name="HB1"} 39: atom[97]={name="HB2"} 39: atom[98]={name="SG"} 39: atom[99]={name="HG"} 39: atom[100]={name="C"} 39: atom[101]={name="O"} 39: atom[102]={name="N"} 39: atom[103]={name="H"} 39: atom[104]={name="CA"} 39: atom[105]={name="HA"} 39: atom[106]={name="CB"} 39: atom[107]={name="HB1"} 39: atom[108]={name="HB2"} 39: atom[109]={name="CG"} 39: atom[110]={name="HG1"} 39: atom[111]={name="HG2"} 39: atom[112]={name="CD"} 39: atom[113]={name="OE1"} 39: atom[114]={name="OE2"} 39: atom[115]={name="C"} 39: atom[116]={name="O"} 39: atom[117]={name="N"} 39: atom[118]={name="H"} 39: atom[119]={name="CA"} 39: atom[120]={name="HA"} 39: atom[121]={name="CB"} 39: atom[122]={name="HB1"} 39: atom[123]={name="HB2"} 39: atom[124]={name="CG"} 39: atom[125]={name="HG"} 39: atom[126]={name="CD1"} 39: atom[127]={name="HD11"} 39: atom[128]={name="HD12"} 39: atom[129]={name="HD13"} 39: atom[130]={name="CD2"} 39: atom[131]={name="HD21"} 39: atom[132]={name="HD22"} 39: atom[133]={name="HD23"} 39: atom[134]={name="C"} 39: atom[135]={name="O"} 39: atom[136]={name="N"} 39: atom[137]={name="H"} 39: atom[138]={name="CA"} 39: atom[139]={name="HA"} 39: atom[140]={name="CB"} 39: atom[141]={name="HB1"} 39: atom[142]={name="HB2"} 39: atom[143]={name="HB3"} 39: atom[144]={name="C"} 39: atom[145]={name="O"} 39: atom[146]={name="N"} 39: atom[147]={name="H"} 39: atom[148]={name="CA"} 39: atom[149]={name="HA"} 39: atom[150]={name="CB"} 39: atom[151]={name="HB1"} 39: atom[152]={name="HB2"} 39: atom[153]={name="HB3"} 39: atom[154]={name="C"} 39: atom[155]={name="O"} 39: type (156): 39: type[0]={name="opls_287",nameB="opls_287"} 39: type[1]={name="opls_290",nameB="opls_290"} 39: type[2]={name="opls_290",nameB="opls_290"} 39: type[3]={name="opls_290",nameB="opls_290"} 39: type[4]={name="opls_293B",nameB="opls_293B"} 39: type[5]={name="opls_140",nameB="opls_140"} 39: type[6]={name="opls_136",nameB="opls_136"} 39: type[7]={name="opls_140",nameB="opls_140"} 39: type[8]={name="opls_140",nameB="opls_140"} 39: type[9]={name="opls_136",nameB="opls_136"} 39: type[10]={name="opls_140",nameB="opls_140"} 39: type[11]={name="opls_140",nameB="opls_140"} 39: type[12]={name="opls_136",nameB="opls_136"} 39: type[13]={name="opls_140",nameB="opls_140"} 39: type[14]={name="opls_140",nameB="opls_140"} 39: type[15]={name="opls_292",nameB="opls_292"} 39: type[16]={name="opls_140",nameB="opls_140"} 39: type[17]={name="opls_140",nameB="opls_140"} 39: type[18]={name="opls_287",nameB="opls_287"} 39: type[19]={name="opls_290",nameB="opls_290"} 39: type[20]={name="opls_290",nameB="opls_290"} 39: type[21]={name="opls_290",nameB="opls_290"} 39: type[22]={name="opls_235",nameB="opls_235"} 39: type[23]={name="opls_236",nameB="opls_236"} 39: type[24]={name="opls_238",nameB="opls_238"} 39: type[25]={name="opls_241",nameB="opls_241"} 39: type[26]={name="opls_224B",nameB="opls_224B"} 39: type[27]={name="opls_140",nameB="opls_140"} 39: type[28]={name="opls_137",nameB="opls_137"} 39: type[29]={name="opls_140",nameB="opls_140"} 39: type[30]={name="opls_135",nameB="opls_135"} 39: type[31]={name="opls_140",nameB="opls_140"} 39: type[32]={name="opls_140",nameB="opls_140"} 39: type[33]={name="opls_140",nameB="opls_140"} 39: type[34]={name="opls_135",nameB="opls_135"} 39: type[35]={name="opls_140",nameB="opls_140"} 39: type[36]={name="opls_140",nameB="opls_140"} 39: type[37]={name="opls_140",nameB="opls_140"} 39: type[38]={name="opls_235",nameB="opls_235"} 39: type[39]={name="opls_236",nameB="opls_236"} 39: type[40]={name="opls_238",nameB="opls_238"} 39: type[41]={name="opls_241",nameB="opls_241"} 39: type[42]={name="opls_224B",nameB="opls_224B"} 39: type[43]={name="opls_140",nameB="opls_140"} 39: type[44]={name="opls_149",nameB="opls_149"} 39: type[45]={name="opls_140",nameB="opls_140"} 39: type[46]={name="opls_140",nameB="opls_140"} 39: type[47]={name="opls_145",nameB="opls_145"} 39: type[48]={name="opls_145",nameB="opls_145"} 39: type[49]={name="opls_146",nameB="opls_146"} 39: type[50]={name="opls_145",nameB="opls_145"} 39: type[51]={name="opls_146",nameB="opls_146"} 39: type[52]={name="opls_145",nameB="opls_145"} 39: type[53]={name="opls_146",nameB="opls_146"} 39: type[54]={name="opls_145",nameB="opls_145"} 39: type[55]={name="opls_146",nameB="opls_146"} 39: type[56]={name="opls_145",nameB="opls_145"} 39: type[57]={name="opls_146",nameB="opls_146"} 39: type[58]={name="opls_235",nameB="opls_235"} 39: type[59]={name="opls_236",nameB="opls_236"} 39: type[60]={name="opls_238",nameB="opls_238"} 39: type[61]={name="opls_241",nameB="opls_241"} 39: type[62]={name="opls_223B",nameB="opls_223B"} 39: type[63]={name="opls_140",nameB="opls_140"} 39: type[64]={name="opls_140",nameB="opls_140"} 39: type[65]={name="opls_235",nameB="opls_235"} 39: type[66]={name="opls_236",nameB="opls_236"} 39: type[67]={name="opls_238",nameB="opls_238"} 39: type[68]={name="opls_241",nameB="opls_241"} 39: type[69]={name="opls_224B",nameB="opls_224B"} 39: type[70]={name="opls_140",nameB="opls_140"} 39: type[71]={name="opls_136",nameB="opls_136"} 39: type[72]={name="opls_140",nameB="opls_140"} 39: type[73]={name="opls_140",nameB="opls_140"} 39: type[74]={name="opls_308",nameB="opls_308"} 39: type[75]={name="opls_140",nameB="opls_140"} 39: type[76]={name="opls_140",nameB="opls_140"} 39: type[77]={name="opls_307",nameB="opls_307"} 39: type[78]={name="opls_140",nameB="opls_140"} 39: type[79]={name="opls_140",nameB="opls_140"} 39: type[80]={name="opls_303",nameB="opls_303"} 39: type[81]={name="opls_304",nameB="opls_304"} 39: type[82]={name="opls_302",nameB="opls_302"} 39: type[83]={name="opls_300",nameB="opls_300"} 39: type[84]={name="opls_301",nameB="opls_301"} 39: type[85]={name="opls_301",nameB="opls_301"} 39: type[86]={name="opls_300",nameB="opls_300"} 39: type[87]={name="opls_301",nameB="opls_301"} 39: type[88]={name="opls_301",nameB="opls_301"} 39: type[89]={name="opls_235",nameB="opls_235"} 39: type[90]={name="opls_236",nameB="opls_236"} 39: type[91]={name="opls_238",nameB="opls_238"} 39: type[92]={name="opls_241",nameB="opls_241"} 39: type[93]={name="opls_224B",nameB="opls_224B"} 39: type[94]={name="opls_140",nameB="opls_140"} 39: type[95]={name="opls_206",nameB="opls_206"} 39: type[96]={name="opls_140",nameB="opls_140"} 39: type[97]={name="opls_140",nameB="opls_140"} 39: type[98]={name="opls_200",nameB="opls_200"} 39: type[99]={name="opls_204",nameB="opls_204"} 39: type[100]={name="opls_235",nameB="opls_235"} 39: type[101]={name="opls_236",nameB="opls_236"} 39: type[102]={name="opls_238",nameB="opls_238"} 39: type[103]={name="opls_241",nameB="opls_241"} 39: type[104]={name="opls_224B",nameB="opls_224B"} 39: type[105]={name="opls_140",nameB="opls_140"} 39: type[106]={name="opls_136",nameB="opls_136"} 39: type[107]={name="opls_140",nameB="opls_140"} 39: type[108]={name="opls_140",nameB="opls_140"} 39: type[109]={name="opls_274",nameB="opls_274"} 39: type[110]={name="opls_140",nameB="opls_140"} 39: type[111]={name="opls_140",nameB="opls_140"} 39: type[112]={name="opls_271",nameB="opls_271"} 39: type[113]={name="opls_272",nameB="opls_272"} 39: type[114]={name="opls_272",nameB="opls_272"} 39: type[115]={name="opls_235",nameB="opls_235"} 39: type[116]={name="opls_236",nameB="opls_236"} 39: type[117]={name="opls_238",nameB="opls_238"} 39: type[118]={name="opls_241",nameB="opls_241"} 39: type[119]={name="opls_224B",nameB="opls_224B"} 39: type[120]={name="opls_140",nameB="opls_140"} 39: type[121]={name="opls_136",nameB="opls_136"} 39: type[122]={name="opls_140",nameB="opls_140"} 39: type[123]={name="opls_140",nameB="opls_140"} 39: type[124]={name="opls_137",nameB="opls_137"} 39: type[125]={name="opls_140",nameB="opls_140"} 39: type[126]={name="opls_135",nameB="opls_135"} 39: type[127]={name="opls_140",nameB="opls_140"} 39: type[128]={name="opls_140",nameB="opls_140"} 39: type[129]={name="opls_140",nameB="opls_140"} 39: type[130]={name="opls_135",nameB="opls_135"} 39: type[131]={name="opls_140",nameB="opls_140"} 39: type[132]={name="opls_140",nameB="opls_140"} 39: type[133]={name="opls_140",nameB="opls_140"} 39: type[134]={name="opls_235",nameB="opls_235"} 39: type[135]={name="opls_236",nameB="opls_236"} 39: type[136]={name="opls_238",nameB="opls_238"} 39: type[137]={name="opls_241",nameB="opls_241"} 39: type[138]={name="opls_224B",nameB="opls_224B"} 39: type[139]={name="opls_140",nameB="opls_140"} 39: type[140]={name="opls_135",nameB="opls_135"} 39: type[141]={name="opls_140",nameB="opls_140"} 39: type[142]={name="opls_140",nameB="opls_140"} 39: type[143]={name="opls_140",nameB="opls_140"} 39: type[144]={name="opls_235",nameB="opls_235"} 39: type[145]={name="opls_236",nameB="opls_236"} 39: type[146]={name="opls_238",nameB="opls_238"} 39: type[147]={name="opls_241",nameB="opls_241"} 39: type[148]={name="opls_224B",nameB="opls_224B"} 39: type[149]={name="opls_140",nameB="opls_140"} 39: type[150]={name="opls_135",nameB="opls_135"} 39: type[151]={name="opls_140",nameB="opls_140"} 39: type[152]={name="opls_140",nameB="opls_140"} 39: type[153]={name="opls_140",nameB="opls_140"} 39: type[154]={name="opls_235",nameB="opls_235"} 39: type[155]={name="opls_236",nameB="opls_236"} 39: residue (10): 39: residue[0]={name="LYS", nr=1, ic=' '} 39: residue[1]={name="VAL", nr=2, ic=' '} 39: residue[2]={name="PHE", nr=3, ic=' '} 39: residue[3]={name="GLY", nr=4, ic=' '} 39: residue[4]={name="ARG", nr=5, ic=' '} 39: residue[5]={name="CYS", nr=6, ic=' '} 39: residue[6]={name="GLU", nr=7, ic=' '} 39: residue[7]={name="LEU", nr=8, ic=' '} 39: residue[8]={name="ALA", nr=9, ic=' '} 39: residue[9]={name="ALA", nr=10, ic=' '} 39: excls: 39: nr=156 39: nra=1828 39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 39: 23, 24, 25, 26} 39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 39: 14, 15, 22, 23, 24} 39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 39: 16, 17, 18, 22} 39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39: 17, 18, 19, 20, 21} 39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39: 19, 20, 21} 39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 39: 25, 26, 27, 28, 38} 39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26} 39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 39: 30, 34, 38, 39, 40} 39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38} 39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 39: 40} 39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39: 34, 35, 36, 37, 38, 39, 40} 39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 39: 40, 41, 42, 43, 44, 58} 39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42} 39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 39: 45, 46, 47, 58, 59, 60} 39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58} 39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 39: 48, 50, 58, 59, 60, 61, 62} 39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 39: 60} 39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 39: 50, 51, 52, 54, 58, 59, 60} 39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 39: 52, 53, 54, 55, 56, 58} 39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 39: 54, 56, 57} 39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56} 39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 39: 55, 56, 57} 39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56} 39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57} 39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57} 39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57} 39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 39: 60, 61, 62, 63, 64, 65} 39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62} 39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 39: 65, 66, 67} 39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65} 39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 39: 68, 69} 39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67} 39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67} 39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 39: 70, 71, 89} 39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69} 39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 39: 72, 73, 74, 89, 90, 91} 39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89} 39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 39: 75, 76, 77, 89, 90, 91, 92, 93} 39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 39: 91} 39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 39: 77, 78, 79, 80, 89, 90, 91} 39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 39: 79, 80, 81, 82, 89} 39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 39: 81, 82, 83, 86} 39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 39: 84, 85, 86, 87, 88} 39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86} 39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 39: 86, 87, 88} 39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86} 39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86} 39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88} 39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88} 39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 39: 90, 91, 92, 93, 94, 95, 100} 39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93} 39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 39: 95, 96, 97, 98, 100, 101, 102} 39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100} 39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 39: 98, 99, 100, 101, 102, 103, 104} 39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 39: 101, 102} 39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 39: 100, 101, 102} 39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99} 39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 39: 101, 102, 103, 104, 105, 106, 115} 39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104} 39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104, 39: 105, 106, 107, 108, 109, 115, 116, 117} 39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106, 39: 115} 39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106, 39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 115, 116, 117} 39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 110, 111, 112, 113, 114, 115, 116, 117} 39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 115} 39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 115} 39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 113, 114, 115} 39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114} 39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114} 39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 115, 116, 117, 118, 119, 120, 121, 134} 39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118, 39: 119} 39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118, 39: 119, 120, 121, 122, 123, 124, 134, 135, 136} 39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121, 39: 134} 39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121, 39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 134, 135, 136} 39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 39: 136} 39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 130, 134} 39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 130, 134} 39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 127, 128, 129, 130, 131, 132, 133, 134} 39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 134, 135, 136, 137, 138, 139, 140, 144} 39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137, 39: 138} 39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137, 39: 138, 139, 140, 141, 142, 143, 144, 145, 146} 39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140, 39: 144} 39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140, 39: 141, 142, 143, 144, 145, 146, 147, 148} 39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146} 39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146} 39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146, 147, 148, 149, 150, 154} 39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147, 39: 148} 39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147, 39: 148, 149, 150, 151, 152, 153, 154, 155} 39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150, 39: 154} 39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150, 39: 151, 152, 153, 154, 155} 39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155} 39: Bond: 39: nr: 468 39: iatoms: 39: 0 type=100 (BONDS) 0 1 39: 1 type=100 (BONDS) 0 2 39: 2 type=100 (BONDS) 0 3 39: 3 type=101 (BONDS) 0 4 39: 4 type=102 (BONDS) 4 5 39: 5 type=103 (BONDS) 4 6 39: 6 type=104 (BONDS) 4 22 39: 7 type=102 (BONDS) 6 7 39: 8 type=102 (BONDS) 6 8 39: 9 type=103 (BONDS) 6 9 39: 10 type=102 (BONDS) 9 10 39: 11 type=102 (BONDS) 9 11 39: 12 type=103 (BONDS) 9 12 39: 13 type=102 (BONDS) 12 13 39: 14 type=102 (BONDS) 12 14 39: 15 type=103 (BONDS) 12 15 39: 16 type=102 (BONDS) 15 16 39: 17 type=102 (BONDS) 15 17 39: 18 type=101 (BONDS) 15 18 39: 19 type=100 (BONDS) 18 19 39: 20 type=100 (BONDS) 18 20 39: 21 type=100 (BONDS) 18 21 39: 22 type=105 (BONDS) 22 23 39: 23 type=106 (BONDS) 22 24 39: 24 type=100 (BONDS) 24 25 39: 25 type=107 (BONDS) 24 26 39: 26 type=102 (BONDS) 26 27 39: 27 type=103 (BONDS) 26 28 39: 28 type=104 (BONDS) 26 38 39: 29 type=102 (BONDS) 28 29 39: 30 type=103 (BONDS) 28 30 39: 31 type=103 (BONDS) 28 34 39: 32 type=102 (BONDS) 30 31 39: 33 type=102 (BONDS) 30 32 39: 34 type=102 (BONDS) 30 33 39: 35 type=102 (BONDS) 34 35 39: 36 type=102 (BONDS) 34 36 39: 37 type=102 (BONDS) 34 37 39: 38 type=105 (BONDS) 38 39 39: 39 type=106 (BONDS) 38 40 39: 40 type=100 (BONDS) 40 41 39: 41 type=107 (BONDS) 40 42 39: 42 type=102 (BONDS) 42 43 39: 43 type=103 (BONDS) 42 44 39: 44 type=104 (BONDS) 42 58 39: 45 type=102 (BONDS) 44 45 39: 46 type=102 (BONDS) 44 46 39: 47 type=108 (BONDS) 44 47 39: 48 type=109 (BONDS) 47 48 39: 49 type=109 (BONDS) 47 50 39: 50 type=110 (BONDS) 48 49 39: 51 type=109 (BONDS) 48 52 39: 52 type=110 (BONDS) 50 51 39: 53 type=109 (BONDS) 50 54 39: 54 type=110 (BONDS) 52 53 39: 55 type=109 (BONDS) 52 56 39: 56 type=110 (BONDS) 54 55 39: 57 type=109 (BONDS) 54 56 39: 58 type=110 (BONDS) 56 57 39: 59 type=105 (BONDS) 58 59 39: 60 type=106 (BONDS) 58 60 39: 61 type=100 (BONDS) 60 61 39: 62 type=107 (BONDS) 60 62 39: 63 type=102 (BONDS) 62 63 39: 64 type=102 (BONDS) 62 64 39: 65 type=104 (BONDS) 62 65 39: 66 type=105 (BONDS) 65 66 39: 67 type=106 (BONDS) 65 67 39: 68 type=100 (BONDS) 67 68 39: 69 type=107 (BONDS) 67 69 39: 70 type=102 (BONDS) 69 70 39: 71 type=103 (BONDS) 69 71 39: 72 type=104 (BONDS) 69 89 39: 73 type=102 (BONDS) 71 72 39: 74 type=102 (BONDS) 71 73 39: 75 type=103 (BONDS) 71 74 39: 76 type=102 (BONDS) 74 75 39: 77 type=102 (BONDS) 74 76 39: 78 type=103 (BONDS) 74 77 39: 79 type=102 (BONDS) 77 78 39: 80 type=102 (BONDS) 77 79 39: 81 type=111 (BONDS) 77 80 39: 82 type=100 (BONDS) 80 81 39: 83 type=112 (BONDS) 80 82 39: 84 type=112 (BONDS) 82 83 39: 85 type=112 (BONDS) 82 86 39: 86 type=100 (BONDS) 83 84 39: 87 type=100 (BONDS) 83 85 39: 88 type=100 (BONDS) 86 87 39: 89 type=100 (BONDS) 86 88 39: 90 type=105 (BONDS) 89 90 39: 91 type=106 (BONDS) 89 91 39: 92 type=100 (BONDS) 91 92 39: 93 type=107 (BONDS) 91 93 39: 94 type=102 (BONDS) 93 94 39: 95 type=103 (BONDS) 93 95 39: 96 type=104 (BONDS) 93 100 39: 97 type=102 (BONDS) 95 96 39: 98 type=102 (BONDS) 95 97 39: 99 type=113 (BONDS) 95 98 39: 100 type=114 (BONDS) 98 99 39: 101 type=105 (BONDS) 100 101 39: 102 type=106 (BONDS) 100 102 39: 103 type=100 (BONDS) 102 103 39: 104 type=107 (BONDS) 102 104 39: 105 type=102 (BONDS) 104 105 39: 106 type=103 (BONDS) 104 106 39: 107 type=104 (BONDS) 104 115 39: 108 type=102 (BONDS) 106 107 39: 109 type=102 (BONDS) 106 108 39: 110 type=103 (BONDS) 106 109 39: 111 type=102 (BONDS) 109 110 39: 112 type=102 (BONDS) 109 111 39: 113 type=104 (BONDS) 109 112 39: 114 type=115 (BONDS) 112 113 39: 115 type=115 (BONDS) 112 114 39: 116 type=105 (BONDS) 115 116 39: 117 type=106 (BONDS) 115 117 39: 118 type=100 (BONDS) 117 118 39: 119 type=107 (BONDS) 117 119 39: 120 type=102 (BONDS) 119 120 39: 121 type=103 (BONDS) 119 121 39: 122 type=104 (BONDS) 119 134 39: 123 type=102 (BONDS) 121 122 39: 124 type=102 (BONDS) 121 123 39: 125 type=103 (BONDS) 121 124 39: 126 type=102 (BONDS) 124 125 39: 127 type=103 (BONDS) 124 126 39: 128 type=103 (BONDS) 124 130 39: 129 type=102 (BONDS) 126 127 39: 130 type=102 (BONDS) 126 128 39: 131 type=102 (BONDS) 126 129 39: 132 type=102 (BONDS) 130 131 39: 133 type=102 (BONDS) 130 132 39: 134 type=102 (BONDS) 130 133 39: 135 type=105 (BONDS) 134 135 39: 136 type=106 (BONDS) 134 136 39: 137 type=100 (BONDS) 136 137 39: 138 type=107 (BONDS) 136 138 39: 139 type=102 (BONDS) 138 139 39: 140 type=103 (BONDS) 138 140 39: 141 type=104 (BONDS) 138 144 39: 142 type=102 (BONDS) 140 141 39: 143 type=102 (BONDS) 140 142 39: 144 type=102 (BONDS) 140 143 39: 145 type=105 (BONDS) 144 145 39: 146 type=106 (BONDS) 144 146 39: 147 type=100 (BONDS) 146 147 39: 148 type=107 (BONDS) 146 148 39: 149 type=102 (BONDS) 148 149 39: 150 type=103 (BONDS) 148 150 39: 151 type=104 (BONDS) 148 154 39: 152 type=102 (BONDS) 150 151 39: 153 type=102 (BONDS) 150 152 39: 154 type=102 (BONDS) 150 153 39: 155 type=105 (BONDS) 154 155 39: G96Bond: 39: nr: 0 39: Morse: 39: nr: 0 39: Cubic Bonds: 39: nr: 0 39: Connect Bonds: 39: nr: 0 39: Harmonic Pot.: 39: nr: 0 39: FENE Bonds: 39: nr: 0 39: Tab. Bonds: 39: nr: 0 39: Tab. Bonds NC: 39: nr: 0 39: Restraint Pot.: 39: nr: 0 39: Angle: 39: nr: 1124 39: iatoms: 39: 0 type=116 (ANGLES) 1 0 2 39: 1 type=116 (ANGLES) 1 0 3 39: 2 type=116 (ANGLES) 1 0 4 39: 3 type=116 (ANGLES) 2 0 3 39: 4 type=116 (ANGLES) 2 0 4 39: 5 type=116 (ANGLES) 3 0 4 39: 6 type=116 (ANGLES) 0 4 5 39: 7 type=117 (ANGLES) 0 4 6 39: 8 type=117 (ANGLES) 0 4 22 39: 9 type=118 (ANGLES) 5 4 6 39: 10 type=116 (ANGLES) 5 4 22 39: 11 type=119 (ANGLES) 6 4 22 39: 12 type=118 (ANGLES) 4 6 7 39: 13 type=118 (ANGLES) 4 6 8 39: 14 type=120 (ANGLES) 4 6 9 39: 15 type=121 (ANGLES) 7 6 8 39: 16 type=118 (ANGLES) 7 6 9 39: 17 type=118 (ANGLES) 8 6 9 39: 18 type=118 (ANGLES) 6 9 10 39: 19 type=118 (ANGLES) 6 9 11 39: 20 type=120 (ANGLES) 6 9 12 39: 21 type=121 (ANGLES) 10 9 11 39: 22 type=118 (ANGLES) 10 9 12 39: 23 type=118 (ANGLES) 11 9 12 39: 24 type=118 (ANGLES) 9 12 13 39: 25 type=118 (ANGLES) 9 12 14 39: 26 type=120 (ANGLES) 9 12 15 39: 27 type=121 (ANGLES) 13 12 14 39: 28 type=118 (ANGLES) 13 12 15 39: 29 type=118 (ANGLES) 14 12 15 39: 30 type=118 (ANGLES) 12 15 16 39: 31 type=118 (ANGLES) 12 15 17 39: 32 type=117 (ANGLES) 12 15 18 39: 33 type=121 (ANGLES) 16 15 17 39: 34 type=116 (ANGLES) 16 15 18 39: 35 type=116 (ANGLES) 17 15 18 39: 36 type=116 (ANGLES) 15 18 19 39: 37 type=116 (ANGLES) 15 18 20 39: 38 type=116 (ANGLES) 15 18 21 39: 39 type=116 (ANGLES) 19 18 20 39: 40 type=116 (ANGLES) 19 18 21 39: 41 type=116 (ANGLES) 20 18 21 39: 42 type=122 (ANGLES) 4 22 23 39: 43 type=123 (ANGLES) 4 22 24 39: 44 type=124 (ANGLES) 23 22 24 39: 45 type=125 (ANGLES) 22 24 25 39: 46 type=126 (ANGLES) 22 24 26 39: 47 type=127 (ANGLES) 25 24 26 39: 48 type=116 (ANGLES) 24 26 27 39: 49 type=128 (ANGLES) 24 26 28 39: 50 type=129 (ANGLES) 24 26 38 39: 51 type=118 (ANGLES) 27 26 28 39: 52 type=116 (ANGLES) 27 26 38 39: 53 type=119 (ANGLES) 28 26 38 39: 54 type=118 (ANGLES) 26 28 29 39: 55 type=120 (ANGLES) 26 28 30 39: 56 type=120 (ANGLES) 26 28 34 39: 57 type=118 (ANGLES) 29 28 30 39: 58 type=118 (ANGLES) 29 28 34 39: 59 type=120 (ANGLES) 30 28 34 39: 60 type=118 (ANGLES) 28 30 31 39: 61 type=118 (ANGLES) 28 30 32 39: 62 type=118 (ANGLES) 28 30 33 39: 63 type=121 (ANGLES) 31 30 32 39: 64 type=121 (ANGLES) 31 30 33 39: 65 type=121 (ANGLES) 32 30 33 39: 66 type=118 (ANGLES) 28 34 35 39: 67 type=118 (ANGLES) 28 34 36 39: 68 type=118 (ANGLES) 28 34 37 39: 69 type=121 (ANGLES) 35 34 36 39: 70 type=121 (ANGLES) 35 34 37 39: 71 type=121 (ANGLES) 36 34 37 39: 72 type=122 (ANGLES) 26 38 39 39: 73 type=123 (ANGLES) 26 38 40 39: 74 type=124 (ANGLES) 39 38 40 39: 75 type=125 (ANGLES) 38 40 41 39: 76 type=126 (ANGLES) 38 40 42 39: 77 type=127 (ANGLES) 41 40 42 39: 78 type=116 (ANGLES) 40 42 43 39: 79 type=128 (ANGLES) 40 42 44 39: 80 type=129 (ANGLES) 40 42 58 39: 81 type=118 (ANGLES) 43 42 44 39: 82 type=116 (ANGLES) 43 42 58 39: 83 type=119 (ANGLES) 44 42 58 39: 84 type=118 (ANGLES) 42 44 45 39: 85 type=118 (ANGLES) 42 44 46 39: 86 type=130 (ANGLES) 42 44 47 39: 87 type=121 (ANGLES) 45 44 46 39: 88 type=116 (ANGLES) 45 44 47 39: 89 type=116 (ANGLES) 46 44 47 39: 90 type=131 (ANGLES) 44 47 48 39: 91 type=131 (ANGLES) 44 47 50 39: 92 type=132 (ANGLES) 48 47 50 39: 93 type=133 (ANGLES) 47 48 49 39: 94 type=132 (ANGLES) 47 48 52 39: 95 type=133 (ANGLES) 49 48 52 39: 96 type=133 (ANGLES) 47 50 51 39: 97 type=132 (ANGLES) 47 50 54 39: 98 type=133 (ANGLES) 51 50 54 39: 99 type=133 (ANGLES) 48 52 53 39: 100 type=132 (ANGLES) 48 52 56 39: 101 type=133 (ANGLES) 53 52 56 39: 102 type=133 (ANGLES) 50 54 55 39: 103 type=132 (ANGLES) 50 54 56 39: 104 type=133 (ANGLES) 55 54 56 39: 105 type=132 (ANGLES) 52 56 54 39: 106 type=133 (ANGLES) 52 56 57 39: 107 type=133 (ANGLES) 54 56 57 39: 108 type=122 (ANGLES) 42 58 59 39: 109 type=123 (ANGLES) 42 58 60 39: 110 type=124 (ANGLES) 59 58 60 39: 111 type=125 (ANGLES) 58 60 61 39: 112 type=126 (ANGLES) 58 60 62 39: 113 type=127 (ANGLES) 61 60 62 39: 114 type=116 (ANGLES) 60 62 63 39: 115 type=116 (ANGLES) 60 62 64 39: 116 type=129 (ANGLES) 60 62 65 39: 117 type=121 (ANGLES) 63 62 64 39: 118 type=116 (ANGLES) 63 62 65 39: 119 type=116 (ANGLES) 64 62 65 39: 120 type=122 (ANGLES) 62 65 66 39: 121 type=123 (ANGLES) 62 65 67 39: 122 type=124 (ANGLES) 66 65 67 39: 123 type=125 (ANGLES) 65 67 68 39: 124 type=126 (ANGLES) 65 67 69 39: 125 type=127 (ANGLES) 68 67 69 39: 126 type=116 (ANGLES) 67 69 70 39: 127 type=128 (ANGLES) 67 69 71 39: 128 type=129 (ANGLES) 67 69 89 39: 129 type=118 (ANGLES) 70 69 71 39: 130 type=116 (ANGLES) 70 69 89 39: 131 type=119 (ANGLES) 71 69 89 39: 132 type=118 (ANGLES) 69 71 72 39: 133 type=118 (ANGLES) 69 71 73 39: 134 type=120 (ANGLES) 69 71 74 39: 135 type=121 (ANGLES) 72 71 73 39: 136 type=118 (ANGLES) 72 71 74 39: 137 type=118 (ANGLES) 73 71 74 39: 138 type=118 (ANGLES) 71 74 75 39: 139 type=118 (ANGLES) 71 74 76 39: 140 type=120 (ANGLES) 71 74 77 39: 141 type=121 (ANGLES) 75 74 76 39: 142 type=118 (ANGLES) 75 74 77 39: 143 type=118 (ANGLES) 76 74 77 39: 144 type=118 (ANGLES) 74 77 78 39: 145 type=118 (ANGLES) 74 77 79 39: 146 type=117 (ANGLES) 74 77 80 39: 147 type=121 (ANGLES) 78 77 79 39: 148 type=116 (ANGLES) 78 77 80 39: 149 type=116 (ANGLES) 79 77 80 39: 150 type=134 (ANGLES) 77 80 81 39: 151 type=135 (ANGLES) 77 80 82 39: 152 type=133 (ANGLES) 81 80 82 39: 153 type=131 (ANGLES) 80 82 83 39: 154 type=131 (ANGLES) 80 82 86 39: 155 type=131 (ANGLES) 83 82 86 39: 156 type=133 (ANGLES) 82 83 84 39: 157 type=133 (ANGLES) 82 83 85 39: 158 type=133 (ANGLES) 84 83 85 39: 159 type=133 (ANGLES) 82 86 87 39: 160 type=133 (ANGLES) 82 86 88 39: 161 type=133 (ANGLES) 87 86 88 39: 162 type=122 (ANGLES) 69 89 90 39: 163 type=123 (ANGLES) 69 89 91 39: 164 type=124 (ANGLES) 90 89 91 39: 165 type=125 (ANGLES) 89 91 92 39: 166 type=126 (ANGLES) 89 91 93 39: 167 type=127 (ANGLES) 92 91 93 39: 168 type=116 (ANGLES) 91 93 94 39: 169 type=128 (ANGLES) 91 93 95 39: 170 type=129 (ANGLES) 91 93 100 39: 171 type=118 (ANGLES) 94 93 95 39: 172 type=116 (ANGLES) 94 93 100 39: 173 type=119 (ANGLES) 95 93 100 39: 174 type=118 (ANGLES) 93 95 96 39: 175 type=118 (ANGLES) 93 95 97 39: 176 type=136 (ANGLES) 93 95 98 39: 177 type=121 (ANGLES) 96 95 97 39: 178 type=116 (ANGLES) 96 95 98 39: 179 type=116 (ANGLES) 97 95 98 39: 180 type=137 (ANGLES) 95 98 99 39: 181 type=122 (ANGLES) 93 100 101 39: 182 type=123 (ANGLES) 93 100 102 39: 183 type=124 (ANGLES) 101 100 102 39: 184 type=125 (ANGLES) 100 102 103 39: 185 type=126 (ANGLES) 100 102 104 39: 186 type=127 (ANGLES) 103 102 104 39: 187 type=116 (ANGLES) 102 104 105 39: 188 type=128 (ANGLES) 102 104 106 39: 189 type=129 (ANGLES) 102 104 115 39: 190 type=118 (ANGLES) 105 104 106 39: 191 type=116 (ANGLES) 105 104 115 39: 192 type=119 (ANGLES) 106 104 115 39: 193 type=118 (ANGLES) 104 106 107 39: 194 type=118 (ANGLES) 104 106 108 39: 195 type=120 (ANGLES) 104 106 109 39: 196 type=121 (ANGLES) 107 106 108 39: 197 type=118 (ANGLES) 107 106 109 39: 198 type=118 (ANGLES) 108 106 109 39: 199 type=118 (ANGLES) 106 109 110 39: 200 type=118 (ANGLES) 106 109 111 39: 201 type=119 (ANGLES) 106 109 112 39: 202 type=121 (ANGLES) 110 109 111 39: 203 type=116 (ANGLES) 110 109 112 39: 204 type=116 (ANGLES) 111 109 112 39: 205 type=138 (ANGLES) 109 112 113 39: 206 type=138 (ANGLES) 109 112 114 39: 207 type=139 (ANGLES) 113 112 114 39: 208 type=122 (ANGLES) 104 115 116 39: 209 type=123 (ANGLES) 104 115 117 39: 210 type=124 (ANGLES) 116 115 117 39: 211 type=125 (ANGLES) 115 117 118 39: 212 type=126 (ANGLES) 115 117 119 39: 213 type=127 (ANGLES) 118 117 119 39: 214 type=116 (ANGLES) 117 119 120 39: 215 type=128 (ANGLES) 117 119 121 39: 216 type=129 (ANGLES) 117 119 134 39: 217 type=118 (ANGLES) 120 119 121 39: 218 type=116 (ANGLES) 120 119 134 39: 219 type=119 (ANGLES) 121 119 134 39: 220 type=118 (ANGLES) 119 121 122 39: 221 type=118 (ANGLES) 119 121 123 39: 222 type=120 (ANGLES) 119 121 124 39: 223 type=121 (ANGLES) 122 121 123 39: 224 type=118 (ANGLES) 122 121 124 39: 225 type=118 (ANGLES) 123 121 124 39: 226 type=118 (ANGLES) 121 124 125 39: 227 type=120 (ANGLES) 121 124 126 39: 228 type=120 (ANGLES) 121 124 130 39: 229 type=118 (ANGLES) 125 124 126 39: 230 type=118 (ANGLES) 125 124 130 39: 231 type=120 (ANGLES) 126 124 130 39: 232 type=118 (ANGLES) 124 126 127 39: 233 type=118 (ANGLES) 124 126 128 39: 234 type=118 (ANGLES) 124 126 129 39: 235 type=121 (ANGLES) 127 126 128 39: 236 type=121 (ANGLES) 127 126 129 39: 237 type=121 (ANGLES) 128 126 129 39: 238 type=118 (ANGLES) 124 130 131 39: 239 type=118 (ANGLES) 124 130 132 39: 240 type=118 (ANGLES) 124 130 133 39: 241 type=121 (ANGLES) 131 130 132 39: 242 type=121 (ANGLES) 131 130 133 39: 243 type=121 (ANGLES) 132 130 133 39: 244 type=122 (ANGLES) 119 134 135 39: 245 type=123 (ANGLES) 119 134 136 39: 246 type=124 (ANGLES) 135 134 136 39: 247 type=125 (ANGLES) 134 136 137 39: 248 type=126 (ANGLES) 134 136 138 39: 249 type=127 (ANGLES) 137 136 138 39: 250 type=116 (ANGLES) 136 138 139 39: 251 type=128 (ANGLES) 136 138 140 39: 252 type=129 (ANGLES) 136 138 144 39: 253 type=118 (ANGLES) 139 138 140 39: 254 type=116 (ANGLES) 139 138 144 39: 255 type=119 (ANGLES) 140 138 144 39: 256 type=118 (ANGLES) 138 140 141 39: 257 type=118 (ANGLES) 138 140 142 39: 258 type=118 (ANGLES) 138 140 143 39: 259 type=121 (ANGLES) 141 140 142 39: 260 type=121 (ANGLES) 141 140 143 39: 261 type=121 (ANGLES) 142 140 143 39: 262 type=122 (ANGLES) 138 144 145 39: 263 type=123 (ANGLES) 138 144 146 39: 264 type=124 (ANGLES) 145 144 146 39: 265 type=125 (ANGLES) 144 146 147 39: 266 type=126 (ANGLES) 144 146 148 39: 267 type=127 (ANGLES) 147 146 148 39: 268 type=116 (ANGLES) 146 148 149 39: 269 type=128 (ANGLES) 146 148 150 39: 270 type=129 (ANGLES) 146 148 154 39: 271 type=118 (ANGLES) 149 148 150 39: 272 type=116 (ANGLES) 149 148 154 39: 273 type=119 (ANGLES) 150 148 154 39: 274 type=118 (ANGLES) 148 150 151 39: 275 type=118 (ANGLES) 148 150 152 39: 276 type=118 (ANGLES) 148 150 153 39: 277 type=121 (ANGLES) 151 150 152 39: 278 type=121 (ANGLES) 151 150 153 39: 279 type=121 (ANGLES) 152 150 153 39: 280 type=122 (ANGLES) 148 154 155 39: G96Angle: 39: nr: 0 39: Restricted Angles: 39: nr: 0 39: Lin. Angle: 39: nr: 0 39: Bond-Cross: 39: nr: 0 39: BA-Cross: 39: nr: 0 39: U-B: 39: nr: 0 39: Quartic Angles: 39: nr: 0 39: Tab. Angles: 39: nr: 0 39: Proper Dih.: 39: nr: 145 39: iatoms: 39: 0 type=140 (PDIHS) 4 24 22 23 39: 1 type=141 (PDIHS) 22 26 24 25 39: 2 type=140 (PDIHS) 26 40 38 39 39: 3 type=141 (PDIHS) 38 42 40 41 39: 4 type=140 (PDIHS) 42 60 58 59 39: 5 type=142 (PDIHS) 44 47 50 48 39: 6 type=142 (PDIHS) 47 52 48 49 39: 7 type=142 (PDIHS) 47 54 50 51 39: 8 type=142 (PDIHS) 48 56 52 53 39: 9 type=142 (PDIHS) 50 56 54 55 39: 10 type=142 (PDIHS) 52 54 56 57 39: 11 type=141 (PDIHS) 58 62 60 61 39: 12 type=140 (PDIHS) 62 67 65 66 39: 13 type=141 (PDIHS) 65 69 67 68 39: 14 type=140 (PDIHS) 69 91 89 90 39: 15 type=141 (PDIHS) 77 82 80 81 39: 16 type=140 (PDIHS) 80 83 82 86 39: 17 type=141 (PDIHS) 82 84 83 85 39: 18 type=141 (PDIHS) 82 87 86 88 39: 19 type=141 (PDIHS) 89 93 91 92 39: 20 type=140 (PDIHS) 93 102 100 101 39: 21 type=141 (PDIHS) 100 104 102 103 39: 22 type=140 (PDIHS) 104 117 115 116 39: 23 type=140 (PDIHS) 109 113 112 114 39: 24 type=141 (PDIHS) 115 119 117 118 39: 25 type=140 (PDIHS) 119 136 134 135 39: 26 type=141 (PDIHS) 134 138 136 137 39: 27 type=140 (PDIHS) 138 146 144 145 39: 28 type=141 (PDIHS) 144 148 146 147 39: Ryckaert-Bell.: 39: nr: 1565 39: iatoms: 39: 0 type=143 (RBDIHS) 1 0 4 5 39: 1 type=144 (RBDIHS) 1 0 4 6 39: 2 type=144 (RBDIHS) 1 0 4 22 39: 3 type=143 (RBDIHS) 2 0 4 5 39: 4 type=144 (RBDIHS) 2 0 4 6 39: 5 type=144 (RBDIHS) 2 0 4 22 39: 6 type=143 (RBDIHS) 3 0 4 5 39: 7 type=144 (RBDIHS) 3 0 4 6 39: 8 type=144 (RBDIHS) 3 0 4 22 39: 9 type=145 (RBDIHS) 0 4 6 9 39: 10 type=146 (RBDIHS) 22 4 6 9 39: 11 type=147 (RBDIHS) 0 4 6 7 39: 12 type=147 (RBDIHS) 0 4 6 8 39: 13 type=148 (RBDIHS) 5 4 6 7 39: 14 type=148 (RBDIHS) 5 4 6 8 39: 15 type=148 (RBDIHS) 5 4 6 9 39: 16 type=149 (RBDIHS) 22 4 6 7 39: 17 type=149 (RBDIHS) 22 4 6 8 39: 18 type=150 (RBDIHS) 0 4 22 24 39: 19 type=151 (RBDIHS) 6 4 22 24 39: 20 type=148 (RBDIHS) 4 6 9 10 39: 21 type=148 (RBDIHS) 4 6 9 11 39: 22 type=152 (RBDIHS) 4 6 9 12 39: 23 type=148 (RBDIHS) 7 6 9 10 39: 24 type=148 (RBDIHS) 7 6 9 11 39: 25 type=148 (RBDIHS) 7 6 9 12 39: 26 type=148 (RBDIHS) 8 6 9 10 39: 27 type=148 (RBDIHS) 8 6 9 11 39: 28 type=148 (RBDIHS) 8 6 9 12 39: 29 type=148 (RBDIHS) 6 9 12 13 39: 30 type=148 (RBDIHS) 6 9 12 14 39: 31 type=152 (RBDIHS) 6 9 12 15 39: 32 type=148 (RBDIHS) 10 9 12 13 39: 33 type=148 (RBDIHS) 10 9 12 14 39: 34 type=148 (RBDIHS) 10 9 12 15 39: 35 type=148 (RBDIHS) 11 9 12 13 39: 36 type=148 (RBDIHS) 11 9 12 14 39: 37 type=148 (RBDIHS) 11 9 12 15 39: 38 type=148 (RBDIHS) 9 12 15 16 39: 39 type=148 (RBDIHS) 9 12 15 17 39: 40 type=153 (RBDIHS) 9 12 15 18 39: 41 type=148 (RBDIHS) 13 12 15 16 39: 42 type=148 (RBDIHS) 13 12 15 17 39: 43 type=154 (RBDIHS) 13 12 15 18 39: 44 type=148 (RBDIHS) 14 12 15 16 39: 45 type=148 (RBDIHS) 14 12 15 17 39: 46 type=154 (RBDIHS) 14 12 15 18 39: 47 type=144 (RBDIHS) 12 15 18 19 39: 48 type=144 (RBDIHS) 12 15 18 20 39: 49 type=144 (RBDIHS) 12 15 18 21 39: 50 type=143 (RBDIHS) 16 15 18 19 39: 51 type=143 (RBDIHS) 16 15 18 20 39: 52 type=143 (RBDIHS) 16 15 18 21 39: 53 type=143 (RBDIHS) 17 15 18 19 39: 54 type=143 (RBDIHS) 17 15 18 20 39: 55 type=143 (RBDIHS) 17 15 18 21 39: 56 type=155 (RBDIHS) 4 22 24 25 39: 57 type=156 (RBDIHS) 4 22 24 26 39: 58 type=155 (RBDIHS) 23 22 24 25 39: 59 type=157 (RBDIHS) 23 22 24 26 39: 60 type=158 (RBDIHS) 22 24 26 28 39: 61 type=159 (RBDIHS) 22 24 26 38 39: 62 type=160 (RBDIHS) 24 26 28 30 39: 63 type=160 (RBDIHS) 24 26 28 34 39: 64 type=161 (RBDIHS) 38 26 28 30 39: 65 type=161 (RBDIHS) 38 26 28 34 39: 66 type=147 (RBDIHS) 24 26 28 29 39: 67 type=148 (RBDIHS) 27 26 28 29 39: 68 type=148 (RBDIHS) 27 26 28 30 39: 69 type=148 (RBDIHS) 27 26 28 34 39: 70 type=149 (RBDIHS) 38 26 28 29 39: 71 type=150 (RBDIHS) 24 26 38 40 39: 72 type=151 (RBDIHS) 28 26 38 40 39: 73 type=148 (RBDIHS) 26 28 30 31 39: 74 type=148 (RBDIHS) 26 28 30 32 39: 75 type=148 (RBDIHS) 26 28 30 33 39: 76 type=148 (RBDIHS) 29 28 30 31 39: 77 type=148 (RBDIHS) 29 28 30 32 39: 78 type=148 (RBDIHS) 29 28 30 33 39: 79 type=148 (RBDIHS) 34 28 30 31 39: 80 type=148 (RBDIHS) 34 28 30 32 39: 81 type=148 (RBDIHS) 34 28 30 33 39: 82 type=148 (RBDIHS) 26 28 34 35 39: 83 type=148 (RBDIHS) 26 28 34 36 39: 84 type=148 (RBDIHS) 26 28 34 37 39: 85 type=148 (RBDIHS) 29 28 34 35 39: 86 type=148 (RBDIHS) 29 28 34 36 39: 87 type=148 (RBDIHS) 29 28 34 37 39: 88 type=148 (RBDIHS) 30 28 34 35 39: 89 type=148 (RBDIHS) 30 28 34 36 39: 90 type=148 (RBDIHS) 30 28 34 37 39: 91 type=155 (RBDIHS) 26 38 40 41 39: 92 type=156 (RBDIHS) 26 38 40 42 39: 93 type=155 (RBDIHS) 39 38 40 41 39: 94 type=157 (RBDIHS) 39 38 40 42 39: 95 type=158 (RBDIHS) 38 40 42 44 39: 96 type=159 (RBDIHS) 38 40 42 58 39: 97 type=147 (RBDIHS) 40 42 44 45 39: 98 type=147 (RBDIHS) 40 42 44 46 39: 99 type=162 (RBDIHS) 40 42 44 47 39: 100 type=148 (RBDIHS) 43 42 44 45 39: 101 type=148 (RBDIHS) 43 42 44 46 39: 102 type=163 (RBDIHS) 43 42 44 47 39: 103 type=149 (RBDIHS) 58 42 44 45 39: 104 type=149 (RBDIHS) 58 42 44 46 39: 105 type=164 (RBDIHS) 58 42 44 47 39: 106 type=150 (RBDIHS) 40 42 58 60 39: 107 type=151 (RBDIHS) 44 42 58 60 39: 108 type=165 (RBDIHS) 44 47 48 49 39: 109 type=165 (RBDIHS) 44 47 48 52 39: 110 type=165 (RBDIHS) 50 47 48 49 39: 111 type=165 (RBDIHS) 50 47 48 52 39: 112 type=165 (RBDIHS) 44 47 50 51 39: 113 type=165 (RBDIHS) 44 47 50 54 39: 114 type=165 (RBDIHS) 48 47 50 51 39: 115 type=165 (RBDIHS) 48 47 50 54 39: 116 type=165 (RBDIHS) 47 48 52 53 39: 117 type=165 (RBDIHS) 47 48 52 56 39: 118 type=165 (RBDIHS) 49 48 52 53 39: 119 type=165 (RBDIHS) 49 48 52 56 39: 120 type=165 (RBDIHS) 47 50 54 55 39: 121 type=165 (RBDIHS) 47 50 54 56 39: 122 type=165 (RBDIHS) 51 50 54 55 39: 123 type=165 (RBDIHS) 51 50 54 56 39: 124 type=165 (RBDIHS) 48 52 56 54 39: 125 type=165 (RBDIHS) 48 52 56 57 39: 126 type=165 (RBDIHS) 53 52 56 54 39: 127 type=165 (RBDIHS) 53 52 56 57 39: 128 type=165 (RBDIHS) 50 54 56 52 39: 129 type=165 (RBDIHS) 50 54 56 57 39: 130 type=165 (RBDIHS) 55 54 56 52 39: 131 type=165 (RBDIHS) 55 54 56 57 39: 132 type=155 (RBDIHS) 42 58 60 61 39: 133 type=156 (RBDIHS) 42 58 60 62 39: 134 type=155 (RBDIHS) 59 58 60 61 39: 135 type=157 (RBDIHS) 59 58 60 62 39: 136 type=159 (RBDIHS) 58 60 62 65 39: 137 type=150 (RBDIHS) 60 62 65 67 39: 138 type=155 (RBDIHS) 62 65 67 68 39: 139 type=156 (RBDIHS) 62 65 67 69 39: 140 type=155 (RBDIHS) 66 65 67 68 39: 141 type=157 (RBDIHS) 66 65 67 69 39: 142 type=158 (RBDIHS) 65 67 69 71 39: 143 type=159 (RBDIHS) 65 67 69 89 39: 144 type=166 (RBDIHS) 67 69 71 74 39: 145 type=167 (RBDIHS) 89 69 71 74 39: 146 type=147 (RBDIHS) 67 69 71 72 39: 147 type=147 (RBDIHS) 67 69 71 73 39: 148 type=148 (RBDIHS) 70 69 71 72 39: 149 type=148 (RBDIHS) 70 69 71 73 39: 150 type=148 (RBDIHS) 70 69 71 74 39: 151 type=149 (RBDIHS) 89 69 71 72 39: 152 type=149 (RBDIHS) 89 69 71 73 39: 153 type=150 (RBDIHS) 67 69 89 91 39: 154 type=151 (RBDIHS) 71 69 89 91 39: 155 type=148 (RBDIHS) 69 71 74 75 39: 156 type=148 (RBDIHS) 69 71 74 76 39: 157 type=152 (RBDIHS) 69 71 74 77 39: 158 type=148 (RBDIHS) 72 71 74 75 39: 159 type=148 (RBDIHS) 72 71 74 76 39: 160 type=148 (RBDIHS) 72 71 74 77 39: 161 type=148 (RBDIHS) 73 71 74 75 39: 162 type=148 (RBDIHS) 73 71 74 76 39: 163 type=148 (RBDIHS) 73 71 74 77 39: 164 type=148 (RBDIHS) 71 74 77 78 39: 165 type=148 (RBDIHS) 71 74 77 79 39: 166 type=153 (RBDIHS) 71 74 77 80 39: 167 type=148 (RBDIHS) 75 74 77 78 39: 168 type=148 (RBDIHS) 75 74 77 79 39: 169 type=168 (RBDIHS) 75 74 77 80 39: 170 type=148 (RBDIHS) 76 74 77 78 39: 171 type=148 (RBDIHS) 76 74 77 79 39: 172 type=168 (RBDIHS) 76 74 77 80 39: 173 type=169 (RBDIHS) 74 77 80 81 39: 174 type=170 (RBDIHS) 74 77 80 82 39: 175 type=171 (RBDIHS) 78 77 80 82 39: 176 type=171 (RBDIHS) 79 77 80 82 39: 177 type=172 (RBDIHS) 77 80 82 83 39: 178 type=172 (RBDIHS) 77 80 82 86 39: 179 type=173 (RBDIHS) 81 80 82 83 39: 180 type=173 (RBDIHS) 81 80 82 86 39: 181 type=173 (RBDIHS) 80 82 83 84 39: 182 type=173 (RBDIHS) 80 82 83 85 39: 183 type=173 (RBDIHS) 86 82 83 84 39: 184 type=173 (RBDIHS) 86 82 83 85 39: 185 type=173 (RBDIHS) 80 82 86 87 39: 186 type=173 (RBDIHS) 80 82 86 88 39: 187 type=173 (RBDIHS) 83 82 86 87 39: 188 type=173 (RBDIHS) 83 82 86 88 39: 189 type=155 (RBDIHS) 69 89 91 92 39: 190 type=156 (RBDIHS) 69 89 91 93 39: 191 type=155 (RBDIHS) 90 89 91 92 39: 192 type=157 (RBDIHS) 90 89 91 93 39: 193 type=158 (RBDIHS) 89 91 93 95 39: 194 type=159 (RBDIHS) 89 91 93 100 39: 195 type=174 (RBDIHS) 91 93 95 98 39: 196 type=175 (RBDIHS) 100 93 95 98 39: 197 type=147 (RBDIHS) 91 93 95 96 39: 198 type=147 (RBDIHS) 91 93 95 97 39: 199 type=148 (RBDIHS) 94 93 95 96 39: 200 type=148 (RBDIHS) 94 93 95 97 39: 201 type=176 (RBDIHS) 94 93 95 98 39: 202 type=149 (RBDIHS) 100 93 95 96 39: 203 type=149 (RBDIHS) 100 93 95 97 39: 204 type=150 (RBDIHS) 91 93 100 102 39: 205 type=151 (RBDIHS) 95 93 100 102 39: 206 type=177 (RBDIHS) 93 95 98 99 39: 207 type=178 (RBDIHS) 96 95 98 99 39: 208 type=178 (RBDIHS) 97 95 98 99 39: 209 type=155 (RBDIHS) 93 100 102 103 39: 210 type=156 (RBDIHS) 93 100 102 104 39: 211 type=155 (RBDIHS) 101 100 102 103 39: 212 type=157 (RBDIHS) 101 100 102 104 39: 213 type=158 (RBDIHS) 100 102 104 106 39: 214 type=159 (RBDIHS) 100 102 104 115 39: 215 type=179 (RBDIHS) 102 104 106 109 39: 216 type=180 (RBDIHS) 115 104 106 109 39: 217 type=147 (RBDIHS) 102 104 106 107 39: 218 type=147 (RBDIHS) 102 104 106 108 39: 219 type=148 (RBDIHS) 105 104 106 107 39: 220 type=148 (RBDIHS) 105 104 106 108 39: 221 type=148 (RBDIHS) 105 104 106 109 39: 222 type=149 (RBDIHS) 115 104 106 107 39: 223 type=149 (RBDIHS) 115 104 106 108 39: 224 type=150 (RBDIHS) 102 104 115 117 39: 225 type=151 (RBDIHS) 106 104 115 117 39: 226 type=148 (RBDIHS) 104 106 109 110 39: 227 type=148 (RBDIHS) 104 106 109 111 39: 228 type=181 (RBDIHS) 104 106 109 112 39: 229 type=148 (RBDIHS) 107 106 109 110 39: 230 type=148 (RBDIHS) 107 106 109 111 39: 231 type=182 (RBDIHS) 107 106 109 112 39: 232 type=148 (RBDIHS) 108 106 109 110 39: 233 type=148 (RBDIHS) 108 106 109 111 39: 234 type=182 (RBDIHS) 108 106 109 112 39: 235 type=183 (RBDIHS) 106 109 112 113 39: 236 type=183 (RBDIHS) 106 109 112 114 39: 237 type=155 (RBDIHS) 104 115 117 118 39: 238 type=156 (RBDIHS) 104 115 117 119 39: 239 type=155 (RBDIHS) 116 115 117 118 39: 240 type=157 (RBDIHS) 116 115 117 119 39: 241 type=158 (RBDIHS) 115 117 119 121 39: 242 type=159 (RBDIHS) 115 117 119 134 39: 243 type=184 (RBDIHS) 117 119 121 124 39: 244 type=185 (RBDIHS) 134 119 121 124 39: 245 type=147 (RBDIHS) 117 119 121 122 39: 246 type=147 (RBDIHS) 117 119 121 123 39: 247 type=148 (RBDIHS) 120 119 121 122 39: 248 type=148 (RBDIHS) 120 119 121 123 39: 249 type=148 (RBDIHS) 120 119 121 124 39: 250 type=149 (RBDIHS) 134 119 121 122 39: 251 type=149 (RBDIHS) 134 119 121 123 39: 252 type=150 (RBDIHS) 117 119 134 136 39: 253 type=151 (RBDIHS) 121 119 134 136 39: 254 type=148 (RBDIHS) 119 121 124 125 39: 255 type=152 (RBDIHS) 119 121 124 126 39: 256 type=152 (RBDIHS) 119 121 124 130 39: 257 type=148 (RBDIHS) 122 121 124 125 39: 258 type=148 (RBDIHS) 122 121 124 126 39: 259 type=148 (RBDIHS) 122 121 124 130 39: 260 type=148 (RBDIHS) 123 121 124 125 39: 261 type=148 (RBDIHS) 123 121 124 126 39: 262 type=148 (RBDIHS) 123 121 124 130 39: 263 type=148 (RBDIHS) 121 124 126 127 39: 264 type=148 (RBDIHS) 121 124 126 128 39: 265 type=148 (RBDIHS) 121 124 126 129 39: 266 type=148 (RBDIHS) 125 124 126 127 39: 267 type=148 (RBDIHS) 125 124 126 128 39: 268 type=148 (RBDIHS) 125 124 126 129 39: 269 type=148 (RBDIHS) 130 124 126 127 39: 270 type=148 (RBDIHS) 130 124 126 128 39: 271 type=148 (RBDIHS) 130 124 126 129 39: 272 type=148 (RBDIHS) 121 124 130 131 39: 273 type=148 (RBDIHS) 121 124 130 132 39: 274 type=148 (RBDIHS) 121 124 130 133 39: 275 type=148 (RBDIHS) 125 124 130 131 39: 276 type=148 (RBDIHS) 125 124 130 132 39: 277 type=148 (RBDIHS) 125 124 130 133 39: 278 type=148 (RBDIHS) 126 124 130 131 39: 279 type=148 (RBDIHS) 126 124 130 132 39: 280 type=148 (RBDIHS) 126 124 130 133 39: 281 type=155 (RBDIHS) 119 134 136 137 39: 282 type=156 (RBDIHS) 119 134 136 138 39: 283 type=155 (RBDIHS) 135 134 136 137 39: 284 type=157 (RBDIHS) 135 134 136 138 39: 285 type=158 (RBDIHS) 134 136 138 140 39: 286 type=159 (RBDIHS) 134 136 138 144 39: 287 type=147 (RBDIHS) 136 138 140 141 39: 288 type=147 (RBDIHS) 136 138 140 142 39: 289 type=147 (RBDIHS) 136 138 140 143 39: 290 type=148 (RBDIHS) 139 138 140 141 39: 291 type=148 (RBDIHS) 139 138 140 142 39: 292 type=148 (RBDIHS) 139 138 140 143 39: 293 type=149 (RBDIHS) 144 138 140 141 39: 294 type=149 (RBDIHS) 144 138 140 142 39: 295 type=149 (RBDIHS) 144 138 140 143 39: 296 type=150 (RBDIHS) 136 138 144 146 39: 297 type=151 (RBDIHS) 140 138 144 146 39: 298 type=155 (RBDIHS) 138 144 146 147 39: 299 type=156 (RBDIHS) 138 144 146 148 39: 300 type=155 (RBDIHS) 145 144 146 147 39: 301 type=157 (RBDIHS) 145 144 146 148 39: 302 type=158 (RBDIHS) 144 146 148 150 39: 303 type=159 (RBDIHS) 144 146 148 154 39: 304 type=147 (RBDIHS) 146 148 150 151 39: 305 type=147 (RBDIHS) 146 148 150 152 39: 306 type=147 (RBDIHS) 146 148 150 153 39: 307 type=148 (RBDIHS) 149 148 150 151 39: 308 type=148 (RBDIHS) 149 148 150 152 39: 309 type=148 (RBDIHS) 149 148 150 153 39: 310 type=149 (RBDIHS) 154 148 150 151 39: 311 type=149 (RBDIHS) 154 148 150 152 39: 312 type=149 (RBDIHS) 154 148 150 153 39: Restricted Dih.: 39: nr: 0 39: CBT Dih.: 39: nr: 0 39: Fourier Dih.: 39: nr: 0 39: Improper Dih.: 39: nr: 0 39: Improper Dih.: 39: nr: 0 39: Tab. Dih.: 39: nr: 0 39: CMAP Dih.: 39: nr: 0 39: GB 1-2 Pol. (unused): 39: nr: 0 39: GB 1-3 Pol. (unused): 39: nr: 0 39: GB 1-4 Pol. (unused): 39: nr: 0 39: GB Polarization (unused): 39: nr: 0 39: Nonpolar Sol. (unused): 39: nr: 0 39: LJ-14: 39: nr: 1197 39: iatoms: 39: 0 type=186 (LJ14) 0 7 39: 1 type=186 (LJ14) 0 8 39: 2 type=187 (LJ14) 0 9 39: 3 type=188 (LJ14) 0 23 39: 4 type=189 (LJ14) 0 24 39: 5 type=190 (LJ14) 1 5 39: 6 type=190 (LJ14) 1 6 39: 7 type=190 (LJ14) 1 22 39: 8 type=190 (LJ14) 2 5 39: 9 type=190 (LJ14) 2 6 39: 10 type=190 (LJ14) 2 22 39: 11 type=190 (LJ14) 3 5 39: 12 type=190 (LJ14) 3 6 39: 13 type=190 (LJ14) 3 22 39: 14 type=191 (LJ14) 4 10 39: 15 type=191 (LJ14) 4 11 39: 16 type=192 (LJ14) 4 12 39: 17 type=190 (LJ14) 4 25 39: 18 type=192 (LJ14) 4 26 39: 19 type=193 (LJ14) 5 7 39: 20 type=193 (LJ14) 5 8 39: 21 type=191 (LJ14) 5 9 39: 22 type=194 (LJ14) 5 23 39: 23 type=186 (LJ14) 5 24 39: 24 type=191 (LJ14) 6 13 39: 25 type=191 (LJ14) 6 14 39: 26 type=192 (LJ14) 6 15 39: 27 type=195 (LJ14) 6 23 39: 28 type=187 (LJ14) 6 24 39: 29 type=193 (LJ14) 7 10 39: 30 type=193 (LJ14) 7 11 39: 31 type=191 (LJ14) 7 12 39: 32 type=196 (LJ14) 7 22 39: 33 type=193 (LJ14) 8 10 39: 34 type=193 (LJ14) 8 11 39: 35 type=191 (LJ14) 8 12 39: 36 type=196 (LJ14) 8 22 39: 37 type=191 (LJ14) 9 16 39: 38 type=191 (LJ14) 9 17 39: 39 type=187 (LJ14) 9 18 39: 40 type=197 (LJ14) 9 22 39: 41 type=193 (LJ14) 10 13 39: 42 type=193 (LJ14) 10 14 39: 43 type=191 (LJ14) 10 15 39: 44 type=193 (LJ14) 11 13 39: 45 type=193 (LJ14) 11 14 39: 46 type=191 (LJ14) 11 15 39: 47 type=190 (LJ14) 12 19 39: 48 type=190 (LJ14) 12 20 39: 49 type=190 (LJ14) 12 21 39: 50 type=193 (LJ14) 13 16 39: 51 type=193 (LJ14) 13 17 39: 52 type=186 (LJ14) 13 18 39: 53 type=193 (LJ14) 14 16 39: 54 type=193 (LJ14) 14 17 39: 55 type=186 (LJ14) 14 18 39: 56 type=190 (LJ14) 16 19 39: 57 type=190 (LJ14) 16 20 39: 58 type=190 (LJ14) 16 21 39: 59 type=190 (LJ14) 17 19 39: 60 type=190 (LJ14) 17 20 39: 61 type=190 (LJ14) 17 21 39: 62 type=196 (LJ14) 22 27 39: 63 type=197 (LJ14) 22 28 39: 64 type=198 (LJ14) 22 38 39: 65 type=190 (LJ14) 23 25 39: 66 type=195 (LJ14) 23 26 39: 67 type=186 (LJ14) 24 29 39: 68 type=187 (LJ14) 24 30 39: 69 type=187 (LJ14) 24 34 39: 70 type=188 (LJ14) 24 39 39: 71 type=189 (LJ14) 24 40 39: 72 type=190 (LJ14) 25 27 39: 73 type=190 (LJ14) 25 28 39: 74 type=190 (LJ14) 25 38 39: 75 type=191 (LJ14) 26 31 39: 76 type=191 (LJ14) 26 32 39: 77 type=191 (LJ14) 26 33 39: 78 type=191 (LJ14) 26 35 39: 79 type=191 (LJ14) 26 36 39: 80 type=191 (LJ14) 26 37 39: 81 type=190 (LJ14) 26 41 39: 82 type=192 (LJ14) 26 42 39: 83 type=193 (LJ14) 27 29 39: 84 type=191 (LJ14) 27 30 39: 85 type=191 (LJ14) 27 34 39: 86 type=194 (LJ14) 27 39 39: 87 type=186 (LJ14) 27 40 39: 88 type=195 (LJ14) 28 39 39: 89 type=187 (LJ14) 28 40 39: 90 type=193 (LJ14) 29 31 39: 91 type=193 (LJ14) 29 32 39: 92 type=193 (LJ14) 29 33 39: 93 type=193 (LJ14) 29 35 39: 94 type=193 (LJ14) 29 36 39: 95 type=193 (LJ14) 29 37 39: 96 type=196 (LJ14) 29 38 39: 97 type=191 (LJ14) 30 35 39: 98 type=191 (LJ14) 30 36 39: 99 type=191 (LJ14) 30 37 39: 100 type=197 (LJ14) 30 38 39: 101 type=191 (LJ14) 31 34 39: 102 type=191 (LJ14) 32 34 39: 103 type=191 (LJ14) 33 34 39: 104 type=197 (LJ14) 34 38 39: 105 type=196 (LJ14) 38 43 39: 106 type=197 (LJ14) 38 44 39: 107 type=198 (LJ14) 38 58 39: 108 type=190 (LJ14) 39 41 39: 109 type=195 (LJ14) 39 42 39: 110 type=186 (LJ14) 40 45 39: 111 type=186 (LJ14) 40 46 39: 112 type=199 (LJ14) 40 47 39: 113 type=188 (LJ14) 40 59 39: 114 type=189 (LJ14) 40 60 39: 115 type=190 (LJ14) 41 43 39: 116 type=190 (LJ14) 41 44 39: 117 type=190 (LJ14) 41 58 39: 118 type=200 (LJ14) 42 48 39: 119 type=200 (LJ14) 42 50 39: 120 type=190 (LJ14) 42 61 39: 121 type=192 (LJ14) 42 62 39: 122 type=193 (LJ14) 43 45 39: 123 type=193 (LJ14) 43 46 39: 124 type=201 (LJ14) 43 47 39: 125 type=194 (LJ14) 43 59 39: 126 type=186 (LJ14) 43 60 39: 127 type=202 (LJ14) 44 49 39: 128 type=202 (LJ14) 44 51 39: 129 type=200 (LJ14) 44 52 39: 130 type=200 (LJ14) 44 54 39: 131 type=195 (LJ14) 44 59 39: 132 type=187 (LJ14) 44 60 39: 133 type=201 (LJ14) 45 48 39: 134 type=201 (LJ14) 45 50 39: 135 type=196 (LJ14) 45 58 39: 136 type=201 (LJ14) 46 48 39: 137 type=201 (LJ14) 46 50 39: 138 type=196 (LJ14) 46 58 39: 139 type=203 (LJ14) 47 53 39: 140 type=203 (LJ14) 47 55 39: 141 type=204 (LJ14) 47 56 39: 142 type=205 (LJ14) 47 58 39: 143 type=203 (LJ14) 48 51 39: 144 type=204 (LJ14) 48 54 39: 145 type=203 (LJ14) 48 57 39: 146 type=203 (LJ14) 49 50 39: 147 type=206 (LJ14) 49 53 39: 148 type=203 (LJ14) 49 56 39: 149 type=204 (LJ14) 50 52 39: 150 type=203 (LJ14) 50 57 39: 151 type=206 (LJ14) 51 55 39: 152 type=203 (LJ14) 51 56 39: 153 type=203 (LJ14) 52 55 39: 154 type=203 (LJ14) 53 54 39: 155 type=206 (LJ14) 53 57 39: 156 type=206 (LJ14) 55 57 39: 157 type=196 (LJ14) 58 63 39: 158 type=196 (LJ14) 58 64 39: 159 type=198 (LJ14) 58 65 39: 160 type=190 (LJ14) 59 61 39: 161 type=195 (LJ14) 59 62 39: 162 type=188 (LJ14) 60 66 39: 163 type=189 (LJ14) 60 67 39: 164 type=190 (LJ14) 61 63 39: 165 type=190 (LJ14) 61 64 39: 166 type=190 (LJ14) 61 65 39: 167 type=190 (LJ14) 62 68 39: 168 type=192 (LJ14) 62 69 39: 169 type=194 (LJ14) 63 66 39: 170 type=186 (LJ14) 63 67 39: 171 type=194 (LJ14) 64 66 39: 172 type=186 (LJ14) 64 67 39: 173 type=196 (LJ14) 65 70 39: 174 type=197 (LJ14) 65 71 39: 175 type=198 (LJ14) 65 89 39: 176 type=190 (LJ14) 66 68 39: 177 type=195 (LJ14) 66 69 39: 178 type=186 (LJ14) 67 72 39: 179 type=186 (LJ14) 67 73 39: 180 type=187 (LJ14) 67 74 39: 181 type=188 (LJ14) 67 90 39: 182 type=189 (LJ14) 67 91 39: 183 type=190 (LJ14) 68 70 39: 184 type=190 (LJ14) 68 71 39: 185 type=190 (LJ14) 68 89 39: 186 type=191 (LJ14) 69 75 39: 187 type=191 (LJ14) 69 76 39: 188 type=192 (LJ14) 69 77 39: 189 type=190 (LJ14) 69 92 39: 190 type=192 (LJ14) 69 93 39: 191 type=193 (LJ14) 70 72 39: 192 type=193 (LJ14) 70 73 39: 193 type=191 (LJ14) 70 74 39: 194 type=194 (LJ14) 70 90 39: 195 type=186 (LJ14) 70 91 39: 196 type=191 (LJ14) 71 78 39: 197 type=191 (LJ14) 71 79 39: 198 type=187 (LJ14) 71 80 39: 199 type=195 (LJ14) 71 90 39: 200 type=187 (LJ14) 71 91 39: 201 type=193 (LJ14) 72 75 39: 202 type=193 (LJ14) 72 76 39: 203 type=191 (LJ14) 72 77 39: 204 type=196 (LJ14) 72 89 39: 205 type=193 (LJ14) 73 75 39: 206 type=193 (LJ14) 73 76 39: 207 type=191 (LJ14) 73 77 39: 208 type=196 (LJ14) 73 89 39: 209 type=190 (LJ14) 74 81 39: 210 type=207 (LJ14) 74 82 39: 211 type=197 (LJ14) 74 89 39: 212 type=193 (LJ14) 75 78 39: 213 type=193 (LJ14) 75 79 39: 214 type=186 (LJ14) 75 80 39: 215 type=193 (LJ14) 76 78 39: 216 type=193 (LJ14) 76 79 39: 217 type=186 (LJ14) 76 80 39: 218 type=187 (LJ14) 77 83 39: 219 type=187 (LJ14) 77 86 39: 220 type=190 (LJ14) 78 81 39: 221 type=208 (LJ14) 78 82 39: 222 type=190 (LJ14) 79 81 39: 223 type=208 (LJ14) 79 82 39: 224 type=190 (LJ14) 80 84 39: 225 type=190 (LJ14) 80 85 39: 226 type=190 (LJ14) 80 87 39: 227 type=190 (LJ14) 80 88 39: 228 type=190 (LJ14) 81 83 39: 229 type=190 (LJ14) 81 86 39: 230 type=190 (LJ14) 83 87 39: 231 type=190 (LJ14) 83 88 39: 232 type=190 (LJ14) 84 86 39: 233 type=190 (LJ14) 85 86 39: 234 type=196 (LJ14) 89 94 39: 235 type=197 (LJ14) 89 95 39: 236 type=198 (LJ14) 89 100 39: 237 type=190 (LJ14) 90 92 39: 238 type=195 (LJ14) 90 93 39: 239 type=186 (LJ14) 91 96 39: 240 type=186 (LJ14) 91 97 39: 241 type=209 (LJ14) 91 98 39: 242 type=188 (LJ14) 91 101 39: 243 type=189 (LJ14) 91 102 39: 244 type=190 (LJ14) 92 94 39: 245 type=190 (LJ14) 92 95 39: 246 type=190 (LJ14) 92 100 39: 247 type=190 (LJ14) 93 99 39: 248 type=190 (LJ14) 93 103 39: 249 type=192 (LJ14) 93 104 39: 250 type=193 (LJ14) 94 96 39: 251 type=193 (LJ14) 94 97 39: 252 type=210 (LJ14) 94 98 39: 253 type=194 (LJ14) 94 101 39: 254 type=186 (LJ14) 94 102 39: 255 type=195 (LJ14) 95 101 39: 256 type=187 (LJ14) 95 102 39: 257 type=190 (LJ14) 96 99 39: 258 type=196 (LJ14) 96 100 39: 259 type=190 (LJ14) 97 99 39: 260 type=196 (LJ14) 97 100 39: 261 type=211 (LJ14) 98 100 39: 262 type=196 (LJ14) 100 105 39: 263 type=197 (LJ14) 100 106 39: 264 type=198 (LJ14) 100 115 39: 265 type=190 (LJ14) 101 103 39: 266 type=195 (LJ14) 101 104 39: 267 type=186 (LJ14) 102 107 39: 268 type=186 (LJ14) 102 108 39: 269 type=187 (LJ14) 102 109 39: 270 type=188 (LJ14) 102 116 39: 271 type=189 (LJ14) 102 117 39: 272 type=190 (LJ14) 103 105 39: 273 type=190 (LJ14) 103 106 39: 274 type=190 (LJ14) 103 115 39: 275 type=191 (LJ14) 104 110 39: 276 type=191 (LJ14) 104 111 39: 277 type=197 (LJ14) 104 112 39: 278 type=190 (LJ14) 104 118 39: 279 type=192 (LJ14) 104 119 39: 280 type=193 (LJ14) 105 107 39: 281 type=193 (LJ14) 105 108 39: 282 type=191 (LJ14) 105 109 39: 283 type=194 (LJ14) 105 116 39: 284 type=186 (LJ14) 105 117 39: 285 type=195 (LJ14) 106 113 39: 286 type=195 (LJ14) 106 114 39: 287 type=195 (LJ14) 106 116 39: 288 type=187 (LJ14) 106 117 39: 289 type=193 (LJ14) 107 110 39: 290 type=193 (LJ14) 107 111 39: 291 type=196 (LJ14) 107 112 39: 292 type=196 (LJ14) 107 115 39: 293 type=193 (LJ14) 108 110 39: 294 type=193 (LJ14) 108 111 39: 295 type=196 (LJ14) 108 112 39: 296 type=196 (LJ14) 108 115 39: 297 type=197 (LJ14) 109 115 39: 298 type=194 (LJ14) 110 113 39: 299 type=194 (LJ14) 110 114 39: 300 type=194 (LJ14) 111 113 39: 301 type=194 (LJ14) 111 114 39: 302 type=196 (LJ14) 115 120 39: 303 type=197 (LJ14) 115 121 39: 304 type=198 (LJ14) 115 134 39: 305 type=190 (LJ14) 116 118 39: 306 type=195 (LJ14) 116 119 39: 307 type=186 (LJ14) 117 122 39: 308 type=186 (LJ14) 117 123 39: 309 type=187 (LJ14) 117 124 39: 310 type=188 (LJ14) 117 135 39: 311 type=189 (LJ14) 117 136 39: 312 type=190 (LJ14) 118 120 39: 313 type=190 (LJ14) 118 121 39: 314 type=190 (LJ14) 118 134 39: 315 type=191 (LJ14) 119 125 39: 316 type=192 (LJ14) 119 126 39: 317 type=192 (LJ14) 119 130 39: 318 type=190 (LJ14) 119 137 39: 319 type=192 (LJ14) 119 138 39: 320 type=193 (LJ14) 120 122 39: 321 type=193 (LJ14) 120 123 39: 322 type=191 (LJ14) 120 124 39: 323 type=194 (LJ14) 120 135 39: 324 type=186 (LJ14) 120 136 39: 325 type=191 (LJ14) 121 127 39: 326 type=191 (LJ14) 121 128 39: 327 type=191 (LJ14) 121 129 39: 328 type=191 (LJ14) 121 131 39: 329 type=191 (LJ14) 121 132 39: 330 type=191 (LJ14) 121 133 39: 331 type=195 (LJ14) 121 135 39: 332 type=187 (LJ14) 121 136 39: 333 type=193 (LJ14) 122 125 39: 334 type=191 (LJ14) 122 126 39: 335 type=191 (LJ14) 122 130 39: 336 type=196 (LJ14) 122 134 39: 337 type=193 (LJ14) 123 125 39: 338 type=191 (LJ14) 123 126 39: 339 type=191 (LJ14) 123 130 39: 340 type=196 (LJ14) 123 134 39: 341 type=197 (LJ14) 124 134 39: 342 type=193 (LJ14) 125 127 39: 343 type=193 (LJ14) 125 128 39: 344 type=193 (LJ14) 125 129 39: 345 type=193 (LJ14) 125 131 39: 346 type=193 (LJ14) 125 132 39: 347 type=193 (LJ14) 125 133 39: 348 type=191 (LJ14) 126 131 39: 349 type=191 (LJ14) 126 132 39: 350 type=191 (LJ14) 126 133 39: 351 type=191 (LJ14) 127 130 39: 352 type=191 (LJ14) 128 130 39: 353 type=191 (LJ14) 129 130 39: 354 type=196 (LJ14) 134 139 39: 355 type=197 (LJ14) 134 140 39: 356 type=198 (LJ14) 134 144 39: 357 type=190 (LJ14) 135 137 39: 358 type=195 (LJ14) 135 138 39: 359 type=186 (LJ14) 136 141 39: 360 type=186 (LJ14) 136 142 39: 361 type=186 (LJ14) 136 143 39: 362 type=188 (LJ14) 136 145 39: 363 type=189 (LJ14) 136 146 39: 364 type=190 (LJ14) 137 139 39: 365 type=190 (LJ14) 137 140 39: 366 type=190 (LJ14) 137 144 39: 367 type=190 (LJ14) 138 147 39: 368 type=192 (LJ14) 138 148 39: 369 type=193 (LJ14) 139 141 39: 370 type=193 (LJ14) 139 142 39: 371 type=193 (LJ14) 139 143 39: 372 type=194 (LJ14) 139 145 39: 373 type=186 (LJ14) 139 146 39: 374 type=195 (LJ14) 140 145 39: 375 type=187 (LJ14) 140 146 39: 376 type=196 (LJ14) 141 144 39: 377 type=196 (LJ14) 142 144 39: 378 type=196 (LJ14) 143 144 39: 379 type=196 (LJ14) 144 149 39: 380 type=197 (LJ14) 144 150 39: 381 type=198 (LJ14) 144 154 39: 382 type=190 (LJ14) 145 147 39: 383 type=195 (LJ14) 145 148 39: 384 type=186 (LJ14) 146 151 39: 385 type=186 (LJ14) 146 152 39: 386 type=186 (LJ14) 146 153 39: 387 type=188 (LJ14) 146 155 39: 388 type=190 (LJ14) 147 149 39: 389 type=190 (LJ14) 147 150 39: 390 type=190 (LJ14) 147 154 39: 391 type=193 (LJ14) 149 151 39: 392 type=193 (LJ14) 149 152 39: 393 type=193 (LJ14) 149 153 39: 394 type=194 (LJ14) 149 155 39: 395 type=195 (LJ14) 150 155 39: 396 type=196 (LJ14) 151 154 39: 397 type=196 (LJ14) 152 154 39: 398 type=196 (LJ14) 153 154 39: Coulomb-14: 39: nr: 0 39: LJC-14 q: 39: nr: 0 39: LJC Pairs NB: 39: nr: 0 39: LJ (SR): 39: nr: 0 39: Buck.ham (SR): 39: nr: 0 39: LJ (unused): 39: nr: 0 39: B.ham (unused): 39: nr: 0 39: Disper. corr.: 39: nr: 0 39: Coulomb (SR): 39: nr: 0 39: Coul (unused): 39: nr: 0 39: RF excl.: 39: nr: 0 39: Coul. recip.: 39: nr: 0 39: LJ recip.: 39: nr: 0 39: DPD: 39: nr: 0 39: Polarization: 39: nr: 0 39: Water Pol.: 39: nr: 0 39: Thole Pol.: 39: nr: 0 39: Anharm. Pol.: 39: nr: 0 39: Position Rest.: 39: nr: 0 39: Flat-bottom posres: 39: nr: 0 39: Dis. Rest.: 39: nr: 0 39: D.R.Viol. (nm): 39: nr: 0 39: Orient. Rest.: 39: nr: 0 39: Ori. R. RMSD: 39: nr: 0 39: Angle Rest.: 39: nr: 0 39: Angle Rest. Z: 39: nr: 0 39: Dih. Rest.: 39: nr: 0 39: Dih. Rest. Viol.: 39: nr: 0 39: Constraint: 39: nr: 0 39: Constr. No Conn.: 39: nr: 0 39: Settle: 39: nr: 0 39: Virtual site 2: 39: nr: 0 39: Virtual site 2fd: 39: nr: 0 39: Virtual site 3: 39: nr: 0 39: Virtual site 3fd: 39: nr: 0 39: Virtual site 3fad: 39: nr: 0 39: Virtual site 3out: 39: nr: 0 39: Virtual site 4fd: 39: nr: 0 39: Virtual site 4fdn: 39: nr: 0 39: Virtual site N: 39: nr: 0 39: COM Pull En.: 39: nr: 0 39: Density fitting: 39: nr: 0 39: Quantum En.: 39: nr: 0 39: Potential: 39: nr: 0 39: Kinetic En.: 39: nr: 0 39: Total Energy: 39: nr: 0 39: Conserved En.: 39: nr: 0 39: Temperature: 39: nr: 0 39: Vir. Temp. (not used): 39: nr: 0 39: Pres. DC: 39: nr: 0 39: Pressure: 39: nr: 0 39: dH/dl constr.: 39: nr: 0 39: dVremain/dl: 39: nr: 0 39: dEkin/dl: 39: nr: 0 39: dVcoul/dl: 39: nr: 0 39: dVvdw/dl: 39: nr: 0 39: dVbonded/dl: 39: nr: 0 39: dVrestraint/dl: 39: nr: 0 39: dVtemperature/dl: 39: nr: 0 39: grp[T-Coupling ] nr=1, name=[ rest] 39: grp[Energy Mon. ] nr=1, name=[ rest] 39: grp[Acceleration] nr=1, name=[ rest] 39: grp[Freeze ] nr=1, name=[ rest] 39: grp[User1 ] nr=1, name=[ rest] 39: grp[User2 ] nr=1, name=[ rest] 39: grp[VCM ] nr=1, name=[ rest] 39: grp[Compressed X] nr=1, name=[ rest] 39: grp[Or. Res. Fit] nr=1, name=[ rest] 39: grp[QMMM ] nr=1, name=[ rest] 39: grpname (11): 39: grpname[0]={name="System"} 39: grpname[1]={name="Protein"} 39: grpname[2]={name="Protein-H"} 39: grpname[3]={name="C-alpha"} 39: grpname[4]={name="Backbone"} 39: grpname[5]={name="MainChain"} 39: grpname[6]={name="MainChain+Cb"} 39: grpname[7]={name="MainChain+H"} 39: grpname[8]={name="SideChain"} 39: grpname[9]={name="SideChain-H"} 39: grpname[10]={name="rest"} 39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM 39: allocated 0 0 0 0 0 0 0 0 0 0 39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 39: box (3x3): 39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 39: box_rel (3x3): 39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv (3x3): 39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev (3x3): 39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev (3x3): 39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev (3x3): 39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: nosehoover_xi: not available 39: x (156x3): 39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 39: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 39: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 39: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 39: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 39: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 39: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 39: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 39: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 39: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 39: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 39: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 39: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 39: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 39: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 39: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 39: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 39: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 39: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 39: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 39: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 39: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 39: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 39: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 39: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 39: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 39: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 39: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 39: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 39: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 39: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 39: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 39: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 39: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 39: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 39: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 39: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 39: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 39: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 39: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 39: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 39: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 39: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 39: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 39: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 39: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 39: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 39: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 39: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 39: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 39: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 39: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 39: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 39: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 39: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 39: x[ 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0.00000e+00} 39: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: Group statistics 39: T-Coupling : 156 (total 156 atoms) 39: Energy Mon. : 156 (total 156 atoms) 39: Acceleration: 156 (total 156 atoms) 39: Freeze : 156 (total 156 atoms) 39: User1 : 156 (total 156 atoms) 39: User2 : 156 (total 156 atoms) 39: VCM : 156 (total 156 atoms) 39: Compressed X: 156 (total 156 atoms) 39: Or. Res. Fit: 156 (total 156 atoms) 39: QMMM : 156 (total 156 atoms) 39: [ OK ] DumpTest.WorksWithTpr (10 ms) 39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (1 ms) 39: [----------] 2 tests from DumpTest (11 ms total) 39: 39: [----------] 4 tests from ReportMethodsTest 39: 39: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: For a correct single-point energy evaluation with nsteps = 0, use 39: continuation = yes to avoid constraining the input coordinates. 39: 39: Setting the LD random seed to 1274982167 39: Generated 330891 of the 330891 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 330891 of the 330891 1-4 parameter combinations 39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 39: 39: NOTE 2 [file lysozyme.top, line 1465]: 39: System has non-zero total charge: 2.000000 39: Total charge should normally be an integer. See 39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 39: for discussion on how close it should be to an integer. 39: 39: 39: 39: Number of degrees of freedom in T-Coupling group rest is 465.00 39: 39: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: NVE simulation with an initial temperature of zero: will use a Verlet 39: buffer of 10%. Check your energy drift! 39: 39: 39: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: You are using a plain Coulomb cut-off, which might produce artifacts. 39: You might want to consider using PME electrostatics. 39: 39: 39: 39: There were 4 notes 39: Analysing residue names: 39: There are: 10 Protein residues 39: Analysing Protein... 39: This run will generate roughly 0 Mb of data 39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 39: [ RUN ] ReportMethodsTest.WritesCorrectInformation 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms) 39: [ RUN ] ReportMethodsTest.ToolEndToEndTest 39: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: section: Methods 39: subsection: Simulation system 39: A system of 1 molecules (156 atoms) was simulated. 39: 39: subsection: Simulation settings 39: A total of 0 ns were simulated with a time step of 1 fs. 39: Neighbor searching was performed every 10 steps. 39: The Cut-off algorithm was used for electrostatic interactions. 39: with a cut-off of 1 nm. 39: A single cut-off of 1.1 nm was used for Van der Waals interactions. 39: [ OK ] ReportMethodsTest.ToolEndToEndTest (1 ms) 39: [----------] 4 tests from ReportMethodsTest (2 ms total) 39: 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: trr version: GMX_trn_file (single precision) 39: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (13 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (6 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (8 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from gro file '', 6 atoms. 39: Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (6 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 39: -> frame 0 time 0.000 't= 0.00000', 6 atoms 39: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (3 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (6 ms) 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (42 ms total) 39: 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (0 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (0 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from gro file '', 6 atoms. 39: Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 39: Precision of /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 39: -> frame 0 time 0.000 't= 0.00000', 6 atoms 39: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (4 ms) 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (7 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 18 tests from 4 test cases ran. (1892 ms total) 39: [ PASSED ] 18 tests. 39/54 Test #39: ToolUnitTests ....................... Passed 1.93 sec test 40 Start 40: FileIOTests 40: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/FileIOTests.xml" 40: Test timeout computed to be: 30 40: [==========] Running 33 tests from 8 test cases. 40: [----------] Global test environment set-up. 40: [----------] 2 tests from FileMD5Test 40: [ RUN ] FileMD5Test.CanComputeMD5 40: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 40: [----------] 2 tests from FileMD5Test (1 ms total) 40: 40: [----------] 3 tests from MrcSerializer 40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (1 ms) 40: [----------] 3 tests from MrcSerializer (1 ms total) 40: 40: [----------] 4 tests from MrcDensityMap 40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (5 ms) 40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms) 40: [----------] 4 tests from MrcDensityMap (7 ms total) 40: 40: [----------] 8 tests from MrcDensityMapHeaderTest 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.IsSane 40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 40: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 40: 40: [----------] 9 tests from ReadTest 40: [ RUN ] ReadTest.get_eint_ReadsInteger 40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side '0.8' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 40: [ RUN ] ReadTest.get_eint_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 40: [ RUN ] ReadTest.get_eint64_ReadsInteger 40: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side '0.8' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 40: [ RUN ] ReadTest.get_eint64_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 40: [ RUN ] ReadTest.get_ereal_ReadsInteger 40: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_ereal_ReadsFloat 40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 40: [ RUN ] ReadTest.get_ereal_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not a 40: real value 40: 40: 40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 40: [----------] 9 tests from ReadTest (0 ms total) 40: 40: [----------] 1 test from FileIOXdrSerializerTest 40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms) 40: [----------] 1 test from FileIOXdrSerializerTest (1 ms total) 40: 40: [----------] 2 tests from TngTest 40: [ RUN ] TngTest.CanOpenTngFile 40: TNG library: Cannot open file spc2-traj.tng. /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c: 890 40: TNG library: Cannot open file spc2-traj.tng. /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c: 890 40: [ OK ] TngTest.CanOpenTngFile (0 ms) 40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 40: [----------] 2 tests from TngTest (0 ms total) 40: 40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (5 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (1 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (6 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 33 tests from 8 test cases ran. (16 ms total) 40: [ PASSED ] 33 tests. 40/54 Test #40: FileIOTests ......................... Passed 0.06 sec test 41 Start 41: SelectionUnitTests 41: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 41: Test timeout computed to be: 30 41: [==========] Running 192 tests from 11 test cases. 41: [----------] Global test environment set-up. 41: [----------] 1 test from IndexGroupTest 41: [ RUN ] IndexGroupTest.RemovesDuplicates 41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 41: [----------] 1 test from IndexGroupTest (0 ms total) 41: 41: [----------] 15 tests from IndexBlockTest 41: [ RUN ] IndexBlockTest.CreatesUnknownBlock 41: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 41: [ RUN ] IndexBlockTest.CreatesAtomBlock 41: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms) 41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesSingleBlock 41: [ OK ] IndexBlockTest.CreatesSingleBlock (4 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (1 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 41: [----------] 15 tests from IndexBlockTest (6 ms total) 41: 41: [----------] 11 tests from IndexMapTest 41: [ RUN ] IndexMapTest.InitializesAtomBlock 41: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms) 41: [ RUN ] IndexMapTest.InitializesMoleculeBlock 41: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 41: [ RUN ] IndexMapTest.MapsSingleBlock 41: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 41: [ RUN ] IndexMapTest.MapsResidueBlocks 41: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 41: [ RUN ] IndexMapTest.HandlesMultipleRequests 41: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 41: [----------] 11 tests from IndexMapTest (2 ms total) 41: 41: [----------] 3 tests from IndexGroupsAndNamesTest 41: [ RUN ] IndexGroupsAndNamesTest.containsNames 41: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (1 ms) 41: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total) 41: 41: [----------] 15 tests from NeighborhoodSearchTest 41: [ RUN ] NeighborhoodSearchTest.SimpleSearch 41: [ OK ] NeighborhoodSearchTest.SimpleSearch (37 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (34 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchBox 41: [ OK ] NeighborhoodSearchTest.GridSearchBox (7 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (22 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (8 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (2 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (8 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (80 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (4 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 41: [----------] 15 tests from NeighborhoodSearchTest (204 ms total) 41: 41: [----------] 12 tests from PositionCalculationTest 41: [ RUN ] PositionCalculationTest.ComputesAtomPositions 41: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms) 41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms) 41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionMask 41: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms) 41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 41: [----------] 12 tests from PositionCalculationTest (4 ms total) 41: 41: [----------] 29 tests from SelectionCollectionTest 41: [ RUN ] SelectionCollectionTest.HandlesNoSelections 41: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (4 ms) 41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 41: [----------] 29 tests from SelectionCollectionTest (14 ms total) 41: 41: [----------] 14 tests from SelectionCollectionInteractiveTest 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 41: [----------] 14 tests from SelectionCollectionInteractiveTest (7 ms total) 41: 41: [----------] 66 tests from SelectionCollectionDataTest 41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResnr 41: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesChain 41: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMass 41: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesCharge 41: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBeta 41: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResname 41: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (4 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (2 ms) 41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (2 ms) 41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 41: [----------] 66 tests from SelectionCollectionDataTest (63 ms total) 41: 41: [----------] 17 tests from SelectionOptionTest 41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms) 41: [ RUN ] SelectionOptionTest.ChecksEmptySelections 41: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooManySelections 41: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesAdjuster 41: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 41: [----------] 17 tests from SelectionOptionTest (5 ms total) 41: 41: [----------] 9 tests from SelectionFileOptionTest 41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 41: [----------] 9 tests from SelectionFileOptionTest (3 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 192 tests from 11 test cases ran. (310 ms total) 41: [ PASSED ] 192 tests. 41/54 Test #41: SelectionUnitTests .................. Passed 0.36 sec test 42 Start 42: MdrunOutputTests 42: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 42: Test timeout computed to be: 600 42: [==========] Running 12 tests from 5 test cases. 42: [----------] Global test environment set-up. 42: [----------] 1 test from MdrunTest 42: [ RUN ] MdrunTest.WritesHelp 42: [ OK ] MdrunTest.WritesHelp (3 ms) 42: [----------] 1 test from MdrunTest (3 ms total) 42: 42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 42: Setting the LD random seed to -559361 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.005 0.002 195.1 42: (ns/day) (hour/ns) 42: Performance: 72.131 0.333 42: Reading frame 0 time 0.000 42: # Atoms 6 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (197 ms) 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 42: Setting the LD random seed to 1036516351 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.002 0.001 191.3 42: (ns/day) (hour/ns) 42: Performance: 135.904 0.177 42: Reading frame 0 time 0.000 42: # Atoms 6 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (27 ms) 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 42: Setting the LD random seed to -1484794004 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: NOTE: 16 % of the run time was spent in pair search, 42: you might want to increase nstlist (this has no effect on accuracy) 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.050 0.025 199.4 42: (ns/day) (hour/ns) 42: Performance: 6.856 3.501 42: Reading frame 0 time 0.000 42: # Atoms 3 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (47 ms) 42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (271 ms total) 42: 42: [----------] 2 tests from Argon12/OutputFiles 42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 42: that with the Verlet scheme, nstlist has no effect on the accuracy of 42: your simulation. 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: Setting nstcalcenergy (100) equal to nstenergy (4) 42: 42: Generated 1 of the 1 non-bonded parameter combinations 42: Excluding 1 bonded neighbours molecule type 'Argon' 42: Number of degrees of freedom in T-Coupling group System is 33.00 42: 42: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: NVE simulation: will use the initial temperature of 68.810 K for 42: determining the Verlet buffer size 42: 42: 42: There were 3 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'Argon' 42: 16 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.588 0.294 200.0 42: (ns/day) (hour/ns) 42: Performance: 4.994 4.806 42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (317 ms) 42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 42: that with the Verlet scheme, nstlist has no effect on the accuracy of 42: your simulation. 42: 42: 42: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: Setting nstcalcenergy (100) equal to nstenergy (4) 42: 42: Generated 1 of the 1 non-bonded parameter combinations 42: Excluding 1 bonded neighbours molecule type 'Argon' 42: Number of degrees of freedom in T-Coupling group System is 33.00 42: 42: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: NVE simulation: will use the initial temperature of 68.810 K for 42: determining the Verlet buffer size 42: 42: 42: There were 3 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'Argon' 42: 16 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.004 0.002 195.2 42: (ns/day) (hour/ns) 42: Performance: 725.373 0.033 42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (28 ms) 42: [----------] 2 tests from Argon12/OutputFiles (345 ms total) 42: 42: [----------] 3 tests from MdrunCanWrite/Trajectories 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 42: Setting the LD random seed to -1088701189 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.041 0.020 199.2 42: (ns/day) (hour/ns) 42: Performance: 29.609 0.811 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (39 ms) 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 42: Setting the LD random seed to -34670113 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.088 0.044 199.6 42: (ns/day) (hour/ns) 42: Performance: 13.657 1.757 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (143 ms) 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 42: Setting the LD random seed to -29630465 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.006 0.003 194.9 42: (ns/day) (hour/ns) 42: Performance: 193.215 0.124 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (23 ms) 42: [----------] 3 tests from MdrunCanWrite/Trajectories (205 ms total) 42: 42: [----------] 3 tests from MdrunCanWrite/NptTrajectories 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 42: Setting the LD random seed to -1824538727 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.003 0.002 190.9 42: (ns/day) (hour/ns) 42: Performance: 157.400 0.152 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (14 ms) 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 42: Setting the LD random seed to -262727 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.003 0.002 190.9 42: (ns/day) (hour/ns) 42: Performance: 158.780 0.151 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (16 ms) 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 42: Setting the LD random seed to 1458944363 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.003 0.002 190.7 42: (ns/day) (hour/ns) 42: Performance: 154.449 0.155 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (16 ms) 42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (48 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 12 tests from 5 test cases ran. (872 ms total) 42: [ PASSED ] 12 tests. 42/54 Test #42: MdrunOutputTests .................... Passed 0.89 sec test 43 Start 43: MdrunModulesTests 43: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 43: Test timeout computed to be: 600 43: [==========] Running 10 tests from 3 test cases. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from DensityFittingTest 43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 43: Setting the LD random seed to -883589161 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = -3.85654101644806e+03 43: Maximum force = 2.88468568366558e+03 on atom 3 43: Norm of force = 1.07544474716821e+03 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data 43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (193 ms) 43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 43: Setting the LD random seed to -1434363 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = -2.71386626596691e+04 43: Maximum force = 4.34097106676756e+03 on atom 2 43: Norm of force = 1.25497916295893e+03 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data 43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (17 ms) 43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 43: 43: [WARNING] /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. 43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (7 ms) 43: [ RUN ] DensityFittingTest.CheckpointWorks 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 43: Setting nstcalcenergy (100) equal to nstenergy (2) 43: 43: Setting the LD random seed to 1971056547 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 43: NVE simulation: will use the initial temperature of 68.810 K for 43: determining the Verlet buffer size 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting mdrun 'Argon' 43: 2 steps, 0.0 ps. 43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.004 0.002 195.8 43: (ns/day) (hour/ns) 43: Performance: 115.202 0.208 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: 43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting mdrun 'Argon' 43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.002 0.001 188.1 43: (ns/day) (hour/ns) 43: Performance: 519.329 0.046 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (14 ms) 43: [----------] 4 tests from DensityFittingTest (231 ms total) 43: 43: [----------] 4 tests from MimicTest 43: [ RUN ] MimicTest.OneQuantumMol 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -1663576097 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 20 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.000 0.000 187.7 43: (ns/day) (hour/ns) 43: Performance: 370.919 0.065 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.OneQuantumMol (10 ms) 43: [ RUN ] MimicTest.AllQuantumMol 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -371069467 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 20 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.000 0.000 187.3 43: (ns/day) (hour/ns) 43: Performance: 342.198 0.070 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.AllQuantumMol (19 ms) 43: [ RUN ] MimicTest.TwoQuantumMol 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -270977073 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 19 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.000 0.000 187.7 43: (ns/day) (hour/ns) 43: Performance: 348.450 0.069 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.TwoQuantumMol (16 ms) 43: [ RUN ] MimicTest.BondCuts 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -558438657 43: Generated 2211 of the 2211 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 2211 of the 2211 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 43: Number of degrees of freedom in T-Coupling group rest is 66.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: NVE simulation: will use the initial temperature of 300.368 K for 43: determining the Verlet buffer size 43: 43: 43: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/ala.gro' 43: 43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 17 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.000 191.5 43: (ns/day) (hour/ns) 43: Performance: 183.302 0.131 43: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.BondCuts (45 ms) 43: [----------] 4 tests from MimicTest (90 ms total) 43: 43: [----------] 2 tests from WithIntegrator/ImdTest 43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 43: Setting the LD random seed to -1075316941 43: Generated 20503 of the 20503 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 1 43: Generated 17396 of the 20503 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Glycine' 43: 43: NOTE 1 [file glycine_vacuo.top, line 12]: 43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 43: the time step of 2.0e-03 ps. 43: Maybe you forgot to change the constraints mdp option. 43: 43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 43: Number of degrees of freedom in T-Coupling group System is 27.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34 43: 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: IMD: Enabled. This simulation will accept incoming IMD connections. 43: IMD: Pulling from IMD remote is enabled (-imdpull). 43: IMD: Setting port for connection requests to 0. 43: IMD: Setting up incoming socket. 43: IMD: Listening for IMD connection on port 57381. 43: IMD: -imdwait not set, starting simulation. 43: starting mdrun 'Glycine' 43: 2 steps, 0.0 ps. 43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.002 0.001 188.5 43: (ns/day) (hour/ns) 43: Performance: 445.194 0.054 43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (305 ms) 43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 43: 43: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 43: apply to steep. 43: 43: Setting the LD random seed to -558047362 43: Generated 20503 of the 20503 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 1 43: Generated 17396 of the 20503 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Glycine' 43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 43: Number of degrees of freedom in T-Coupling group System is 27.00 43: 43: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: IMD: Enabled. This simulation will accept incoming IMD connections. 43: IMD: Pulling from IMD remote is enabled (-imdpull). 43: IMD: Setting port for connection requests to 0. 43: IMD: Setting up incoming socket. 43: IMD: Listening for IMD connection on port 33099. 43: IMD: -imdwait not set, starting simulation. 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = 1.19770464690297e+03 43: Maximum force = 1.77948604657896e+04 on atom 9 43: Norm of force = 7.87328617833980e+03 43: This run will generate roughly 0 Mb of data 43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (300 ms) 43: [----------] 2 tests from WithIntegrator/ImdTest (605 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 10 tests from 3 test cases ran. (926 ms total) 43: [ PASSED ] 10 tests. 43/54 Test #43: MdrunModulesTests ................... Passed 0.97 sec test 44 Start 44: MdrunIOTests 44: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 44: Test timeout computed to be: 600 44: [==========] Running 51 tests from 9 test cases. 44: [----------] Global test environment set-up. 44: [----------] 3 tests from GromppTest 44: [ RUN ] GromppTest.EmptyMdpFileWorks 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -152028161 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 12.00 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.EmptyMdpFileWorks (12 ms) 44: [ RUN ] GromppTest.SimulatedAnnealingWorks 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -720212386 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Simulated annealing for group rest: Periodic, 4 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 2.0 320.0 44: 4.0 320.0 44: 6.0 298.0 44: Number of degrees of freedom in T-Coupling group rest is 12.00 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.SimulatedAnnealingWorks (4 ms) 44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to 1859826047 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Simulated annealing for group Methanol: Single, 3 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 3.0 280.0 44: 6.0- 270.0 44: Simulated annealing for group SOL: Periodic, 4 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 2.0 320.0 44: 4.0 320.0 44: 6.0 298.0 44: Number of degrees of freedom in T-Coupling group Methanol is 7.20 44: Number of degrees of freedom in T-Coupling group SOL is 4.80 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (12 ms) 44: [----------] 3 tests from GromppTest (28 ms total) 44: 44: [----------] 6 tests from MdrunTerminationTest 44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 44: Setting the LD random seed to -1435422783 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 194.9 44: (ns/day) (hour/ns) 44: Performance: 87.916 0.273 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 188.2 44: (ns/day) (hour/ns) 44: Performance: 266.789 0.090 44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (205 ms) 44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 44: Setting the LD random seed to -269568286 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 1, rlist from 1.025 to 1 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 100 steps, 0.1 ps. 44: 44: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: NOTE: 36 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.066 0.033 199.6 44: (ns/day) (hour/ns) 44: Performance: 5.194 4.621 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 102 44: Writing statusfile with starting step 0 and length 102 steps... 44: time 0.000 and length 0.102 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.024 0.012 199.0 44: (ns/day) (hour/ns) 44: Performance: 737.722 0.033 44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (71 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 44: Setting the LD random seed to -33686530 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 188.6 44: (ns/day) (hour/ns) 44: Performance: 221.328 0.108 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 195.1 44: (ns/day) (hour/ns) 44: Performance: 274.675 0.087 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 6 44: Writing statusfile with starting step 0 and length 6 steps... 44: time 0.000 and length 0.006 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 194.4 44: (ns/day) (hour/ns) 44: Performance: 228.828 0.105 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 8 44: Writing statusfile with starting step 0 and length 8 steps... 44: time 0.000 and length 0.008 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 194.3 44: (ns/day) (hour/ns) 44: Performance: 257.134 0.093 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: NOTE: 26 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.000 0.000 178.4 44: (ns/day) (hour/ns) 44: Performance: 632.440 0.038 44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (95 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 44: Setting the LD random seed to -1075318959 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 187.9 44: (ns/day) (hour/ns) 44: Performance: 254.665 0.094 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.2 44: (ns/day) (hour/ns) 44: Performance: 373.750 0.064 44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (41 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 44: Setting the LD random seed to -33604169 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 187.6 44: (ns/day) (hour/ns) 44: Performance: 234.758 0.102 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (17 ms) 44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 44: Setting the LD random seed to -1653342217 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 188.4 44: (ns/day) (hour/ns) 44: Performance: 264.839 0.091 44: Reading toplogy and stuff from /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 194.5 44: (ns/day) (hour/ns) 44: Performance: 245.077 0.098 44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (31 ms) 44: [----------] 6 tests from MdrunTerminationTest (461 ms total) 44: 44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.028 0.014 199.0 44: (ns/day) (hour/ns) 44: Performance: 103.430 0.232 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 199.0 44: (ns/day) (hour/ns) 44: Performance: 57.350 0.418 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.025 0.013 198.9 44: (ns/day) (hour/ns) 44: Performance: 61.169 0.392 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (63 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.028 0.014 199.1 44: (ns/day) (hour/ns) 44: Performance: 104.950 0.229 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 198.6 44: (ns/day) (hour/ns) 44: Performance: 136.196 0.176 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 195.7 44: (ns/day) (hour/ns) 44: Performance: 463.741 0.052 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (50 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.5 44: (ns/day) (hour/ns) 44: Performance: 943.574 0.025 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 190.7 44: (ns/day) (hour/ns) 44: Performance: 557.806 0.043 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.7 44: (ns/day) (hour/ns) 44: Performance: 647.378 0.037 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (44 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.2 44: (ns/day) (hour/ns) 44: Performance: 845.306 0.028 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.7 44: (ns/day) (hour/ns) 44: Performance: 666.835 0.036 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.5 44: (ns/day) (hour/ns) 44: Performance: 557.520 0.043 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (35 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.028 0.014 199.0 44: (ns/day) (hour/ns) 44: Performance: 106.071 0.226 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.025 0.013 199.0 44: (ns/day) (hour/ns) 44: Performance: 61.598 0.390 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.0 44: (ns/day) (hour/ns) 44: Performance: 596.578 0.040 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (59 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 197.3 44: (ns/day) (hour/ns) 44: Performance: 701.582 0.034 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 196.0 44: (ns/day) (hour/ns) 44: Performance: 503.627 0.048 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 199.4 44: (ns/day) (hour/ns) 44: Performance: 57.062 0.421 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (54 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 192.2 44: (ns/day) (hour/ns) 44: Performance: 781.900 0.031 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 191.0 44: (ns/day) (hour/ns) 44: Performance: 555.999 0.043 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 190.9 44: (ns/day) (hour/ns) 44: Performance: 542.858 0.044 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (64 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.754 to 0.9 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 192.6 44: (ns/day) (hour/ns) 44: Performance: 778.344 0.031 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.754 to 0.9 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 190.3 44: (ns/day) (hour/ns) 44: Performance: 520.922 0.046 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.754 to 0.9 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 191.5 44: (ns/day) (hour/ns) 44: Performance: 560.972 0.043 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (56 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.033 0.017 198.8 44: (ns/day) (hour/ns) 44: Performance: 88.983 0.270 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 193.2 44: (ns/day) (hour/ns) 44: Performance: 253.280 0.095 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.030 0.015 198.2 44: (ns/day) (hour/ns) 44: Performance: 51.689 0.464 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (180 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.034 0.017 198.9 44: (ns/day) (hour/ns) 44: Performance: 87.015 0.276 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.029 0.014 198.4 44: (ns/day) (hour/ns) 44: Performance: 53.938 0.445 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.044 0.022 199.0 44: (ns/day) (hour/ns) 44: Performance: 35.010 0.686 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (183 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.055 0.028 199.2 44: (ns/day) (hour/ns) 44: Performance: 53.172 0.451 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 193.3 44: (ns/day) (hour/ns) 44: Performance: 327.459 0.073 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 193.7 44: (ns/day) (hour/ns) 44: Performance: 317.173 0.076 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (331 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 198.6 44: (ns/day) (hour/ns) 44: Performance: 113.388 0.212 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 194.6 44: (ns/day) (hour/ns) 44: Performance: 261.296 0.092 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.038 0.019 199.0 44: (ns/day) (hour/ns) 44: Performance: 40.582 0.591 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (219 ms) 44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1338 ms total) 44: 44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.034 0.017 198.4 44: (ns/day) (hour/ns) 44: Performance: 85.402 0.281 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.022 0.011 198.1 44: (ns/day) (hour/ns) 44: Performance: 71.599 0.335 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 192.3 44: (ns/day) (hour/ns) 44: Performance: 295.612 0.081 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (168 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.031 0.015 199.3 44: (ns/day) (hour/ns) 44: Performance: 95.525 0.251 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.9 44: (ns/day) (hour/ns) 44: Performance: 281.018 0.085 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: NOTE: 53 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.045 0.023 199.5 44: (ns/day) (hour/ns) 44: Performance: 34.185 0.702 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (178 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.807 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.025 0.012 198.2 44: (ns/day) (hour/ns) 44: Performance: 118.843 0.202 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.807 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 197.3 44: (ns/day) (hour/ns) 44: Performance: 119.115 0.201 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.807 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 197.1 44: (ns/day) (hour/ns) 44: Performance: 118.608 0.202 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (201 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.017 0.009 197.6 44: (ns/day) (hour/ns) 44: Performance: 172.016 0.140 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 193.1 44: (ns/day) (hour/ns) 44: Performance: 314.633 0.076 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.029 0.015 198.8 44: (ns/day) (hour/ns) 44: Performance: 52.555 0.457 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (193 ms) 44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (740 ms total) 44: 44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 192.5 44: (ns/day) (hour/ns) 44: Performance: 957.655 0.025 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 192.0 44: (ns/day) (hour/ns) 44: Performance: 633.668 0.038 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.2 44: (ns/day) (hour/ns) 44: Performance: 749.940 0.032 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (41 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.4 44: (ns/day) (hour/ns) 44: Performance: 886.416 0.027 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.3 44: (ns/day) (hour/ns) 44: Performance: 547.322 0.044 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: NOTE: 86 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.019 0.009 198.4 44: (ns/day) (hour/ns) 44: Performance: 82.195 0.292 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (42 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 192.6 44: (ns/day) (hour/ns) 44: Performance: 848.333 0.028 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.2 44: (ns/day) (hour/ns) 44: Performance: 667.518 0.036 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.025 0.013 198.7 44: (ns/day) (hour/ns) 44: Performance: 61.377 0.391 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (62 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.5 44: (ns/day) (hour/ns) 44: Performance: 973.699 0.025 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.7 44: (ns/day) (hour/ns) 44: Performance: 524.187 0.046 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.018 0.009 198.9 44: (ns/day) (hour/ns) 44: Performance: 84.057 0.286 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (65 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.028 0.014 199.4 44: (ns/day) (hour/ns) 44: Performance: 105.437 0.228 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 196.8 44: (ns/day) (hour/ns) 44: Performance: 467.597 0.051 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.019 0.009 198.8 44: (ns/day) (hour/ns) 44: Performance: 81.863 0.293 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (47 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.019 0.010 198.3 44: (ns/day) (hour/ns) 44: Performance: 151.010 0.159 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 192.7 44: (ns/day) (hour/ns) 44: Performance: 625.406 0.038 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.8 44: (ns/day) (hour/ns) 44: Performance: 558.283 0.043 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (42 ms) 44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (300 ms total) 44: 44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.2 44: (ns/day) (hour/ns) 44: Performance: 865.738 0.028 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.019 0.009 198.7 44: (ns/day) (hour/ns) 44: Performance: 83.282 0.288 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 198.8 44: (ns/day) (hour/ns) 44: Performance: 59.404 0.404 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (53 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.1 44: (ns/day) (hour/ns) 44: Performance: 955.575 0.025 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.5 44: (ns/day) (hour/ns) 44: Performance: 662.635 0.036 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 190.8 44: (ns/day) (hour/ns) 44: Performance: 593.754 0.040 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (35 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.2 44: (ns/day) (hour/ns) 44: Performance: 881.218 0.027 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.013 199.0 44: (ns/day) (hour/ns) 44: Performance: 57.615 0.417 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.043 0.022 199.2 44: (ns/day) (hour/ns) 44: Performance: 35.995 0.667 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (58 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 196.7 44: (ns/day) (hour/ns) 44: Performance: 776.774 0.031 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 199.5 44: (ns/day) (hour/ns) 44: Performance: 56.613 0.424 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.028 0.014 199.4 44: (ns/day) (hour/ns) 44: Performance: 55.961 0.429 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (57 ms) 44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (203 ms total) 44: 44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 192.7 44: (ns/day) (hour/ns) 44: Performance: 977.717 0.025 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.013 199.1 44: (ns/day) (hour/ns) 44: Performance: 58.180 0.413 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 189.9 44: (ns/day) (hour/ns) 44: Performance: 669.161 0.036 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (46 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 191.4 44: (ns/day) (hour/ns) 44: Performance: 967.582 0.025 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 198.8 44: (ns/day) (hour/ns) 44: Performance: 57.198 0.420 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 198.8 44: (ns/day) (hour/ns) 44: Performance: 60.615 0.396 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (56 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 192.8 44: (ns/day) (hour/ns) 44: Performance: 886.927 0.027 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 191.0 44: (ns/day) (hour/ns) 44: Performance: 615.608 0.039 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.025 0.013 199.0 44: (ns/day) (hour/ns) 44: Performance: 61.262 0.392 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (48 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 193.0 44: (ns/day) (hour/ns) 44: Performance: 974.469 0.025 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 192.0 44: (ns/day) (hour/ns) 44: Performance: 530.151 0.045 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 199.0 44: (ns/day) (hour/ns) 44: Performance: 57.120 0.420 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (50 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: 44: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Using Berendsen pressure coupling invalidates the true ensemble for the 44: thermostat 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: There was 1 warning 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: 44: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Using Berendsen pressure coupling invalidates the true ensemble for the 44: thermostat 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: There was 1 warning 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: NOTE: 58 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.028 0.014 198.9 44: (ns/day) (hour/ns) 44: Performance: 104.674 0.229 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 190.9 44: (ns/day) (hour/ns) 44: Performance: 478.014 0.050 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 199.0 44: (ns/day) (hour/ns) 44: Performance: 57.128 0.420 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (64 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 192.8 44: (ns/day) (hour/ns) 44: Performance: 795.531 0.030 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: NOTE: 89 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 199.0 44: (ns/day) (hour/ns) 44: Performance: 57.076 0.420 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 198.9 44: (ns/day) (hour/ns) 44: Performance: 57.056 0.421 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (64 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: NOTE: 86 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.028 0.014 199.1 44: (ns/day) (hour/ns) 44: Performance: 104.479 0.230 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 191.7 44: (ns/day) (hour/ns) 44: Performance: 517.697 0.046 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 199.0 44: (ns/day) (hour/ns) 44: Performance: 57.286 0.419 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (63 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.028 0.014 198.9 44: (ns/day) (hour/ns) 44: Performance: 104.569 0.230 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 198.8 44: (ns/day) (hour/ns) 44: Performance: 56.670 0.424 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 199.1 44: (ns/day) (hour/ns) 44: Performance: 57.051 0.421 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (65 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.028 0.014 199.5 44: (ns/day) (hour/ns) 44: Performance: 105.214 0.228 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 199.3 44: (ns/day) (hour/ns) 44: Performance: 58.699 0.409 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.001 196.7 44: (ns/day) (hour/ns) 44: Performance: 567.117 0.042 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (54 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms) 44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (510 ms total) 44: 44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 193.5 44: (ns/day) (hour/ns) 44: Performance: 743.225 0.032 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 192.7 44: (ns/day) (hour/ns) 44: Performance: 472.817 0.051 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 192.5 44: (ns/day) (hour/ns) 44: Performance: 465.462 0.052 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (66 ms) 44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (66 ms total) 44: 44: [----------] 3 tests from Checking/InitialConstraintsTest 44: [ RUN ] Checking/InitialConstraintsTest.Works/0 44: Setting the LD random seed to -1649150087 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: NOTE: 77 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.7 44: (ns/day) (hour/ns) 44: Performance: 41.575 0.577 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (19 ms) 44: [ RUN ] Checking/InitialConstraintsTest.Works/1 44: Setting the LD random seed to 1833949149 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 199.2 44: (ns/day) (hour/ns) 44: Performance: 13.071 1.836 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (23 ms) 44: [ RUN ] Checking/InitialConstraintsTest.Works/2 44: 44: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: Integrator method md-vv-avek is implemented primarily for validation 44: purposes; for molecular dynamics, you should probably be using md or md-vv 44: 44: Setting the LD random seed to -277611189 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.002 0.001 187.8 44: (ns/day) (hour/ns) 44: Performance: 171.342 0.140 44: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (17 ms) 44: [----------] 3 tests from Checking/InitialConstraintsTest (59 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 51 tests from 9 test cases ran. (3706 ms total) 44: [ PASSED ] 51 tests. 44/54 Test #44: MdrunIOTests ........................ Passed 3.77 sec test 45 Start 45: MdrunTests 45: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunTests.xml" 45: Test timeout computed to be: 600 45: [==========] Running 24 tests from 7 test cases. 45: [----------] Global test environment set-up. 45: [----------] 1 test from DispersionCorrectionTest 45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to -402817052 45: Generated 2145 of the 2145 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 2145 of the 2145 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 45: Cleaning up constraints and constant bonded interactions with virtual sites 45: Converted 3 Bonds with virtual sites to connections, 7 left 45: Removed 18 Angles with virtual sites, 21 left 45: Removed 10 Proper Dih.s with virtual sites, 44 left 45: Converted 12 Constraints with virtual sites to connections, 0 left 45: Number of degrees of freedom in T-Coupling group System is 30.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: There are 9 non-linear virtual site constructions. Their contribution to 45: the energy error is approximated. In most cases this does not affect the 45: error significantly. 45: 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 10 to 40, rlist from 1.019 to 1.138 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Alanine dipeptide in vacuo' 45: 200 steps, 0.4 ps. 45: turning H bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.128 0.064 199.7 45: (ns/day) (hour/ns) 45: Performance: 542.820 0.044 45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (335 ms) 45: [----------] 1 test from DispersionCorrectionTest (335 ms total) 45: 45: [----------] 1 test from OriresTest 45: [ RUN ] OriresTest.OriresCanRun 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to -85115393 45: Generated 2145 of the 2145 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 2145 of the 2145 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 518.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: 45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 45: Changing nstlist from 10 to 25, rlist from 1.059 to 1.178 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 45: 10 steps, 0.0 ps. 45: turning H bonds into constraints... 45: turning H bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.019 0.009 198.0 45: (ns/day) (hour/ns) 45: Performance: 201.078 0.119 45: [ OK ] OriresTest.OriresCanRun (555 ms) 45: [----------] 1 test from OriresTest (555 ms total) 45: 45: [----------] 3 tests from PmeTest 45: [ RUN ] PmeTest.ReproducesEnergies 45: Setting the LD random seed to -286265422 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group rest is 12.00 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 45: NVE simulation: will use the initial temperature of 1046.791 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.112 0.056 199.7 45: (ns/day) (hour/ns) 45: Performance: 32.494 0.739 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.065 0.032 199.5 45: (ns/day) (hour/ns) 45: Performance: 56.050 0.428 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.064 0.032 199.5 45: (ns/day) (hour/ns) 45: Performance: 56.645 0.424 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (468 ms) 45: [ RUN ] PmeTest.ScalesTheBox 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -1493205521 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group rest is 12.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: NVE simulation: will use the initial temperature of 1046.791 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 0 steps, 0.0 ps. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.002 0.001 186.3 45: (ns/day) (hour/ns) 45: Performance: 89.104 0.269 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 45: This run will generate roughly 0 Mb of data 45: [ OK ] PmeTest.ScalesTheBox (36 ms) 45: [ RUN ] PmeTest.ScalesTheBoxWithWalls 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to 2139090109 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Searching the wall atom type(s) 45: Number of degrees of freedom in T-Coupling group rest is 13.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: NVE simulation: will use the initial temperature of 966.268 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 0 steps, 0.0 ps. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.006 0.003 193.5 45: (ns/day) (hour/ns) 45: Performance: 26.398 0.909 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 45: This run will generate roughly 0 Mb of data 45: [ OK ] PmeTest.ScalesTheBoxWithWalls (749 ms) 45: [----------] 3 tests from PmeTest (1253 ms total) 45: 45: [----------] 1 test from CompelTest 45: [ RUN ] CompelTest.SwapCanRun 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to -536921365 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Protein' 45: Excluding 3 bonded neighbours molecule type 'OCT' 45: Excluding 1 bonded neighbours molecule type 'NA' 45: Excluding 1 bonded neighbours molecule type 'CL' 45: Excluding 3 bonded neighbours molecule type 'Protein' 45: Excluding 3 bonded neighbours molecule type 'OCT' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Split0 group 'Ch0' contains 83 atoms. 45: Split1 group 'Ch1' contains 83 atoms. 45: Solvent group 'SOL' contains 11931 atoms. 45: Swap group 'NA+' contains 19 atoms. 45: Swap group 'CL-' contains 19 atoms. 45: Number of degrees of freedom in T-Coupling group System is 27869.00 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: Removing center of mass motion in the presence of position restraints 45: might cause artifacts. When you are using position restraints to 45: equilibrate a macro-molecule, the artifacts are usually negligible. 45: 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: SWAP: Determining initial numbers of ions per compartment. 45: SWAP: Setting pointers for checkpoint writing 45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 45: starting mdrun 'Channel_coco in octane membrane' 45: 2 steps, 0.0 ps. 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 1 Mb of data 45: 45: Writing final coordinates. 45: 45: NOTE: 37 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 1.137 0.568 200.0 45: (ns/day) (hour/ns) 45: Performance: 2.280 10.527 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: SWAP: Setting pointers for checkpoint writing 45: SWAP: Copying channel fluxes from checkpoint file data 45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 45: starting mdrun 'Channel_coco in octane membrane' 45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 45: 45: Writing final coordinates. 45: 45: NOTE: 24 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.818 0.409 199.9 45: (ns/day) (hour/ns) 45: Performance: 3.167 7.579 45: [ OK ] CompelTest.SwapCanRun (2029 ms) 45: [----------] 1 test from CompelTest (2029 ms total) 45: 45: [----------] 6 tests from BondedInteractionsTest 45: [ RUN ] BondedInteractionsTest.NormalBondWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -234918473 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 2 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 18 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 186.5 45: (ns/day) (hour/ns) 45: Performance: 252.008 0.095 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalBondWorks (47 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to 1605877165 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 2 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 19 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 186.4 45: (ns/day) (hour/ns) 45: Performance: 283.337 0.085 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (16 ms) 45: [ RUN ] BondedInteractionsTest.NormalAngleWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -1694507015 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 20 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.000 0.000 185.4 45: (ns/day) (hour/ns) 45: Performance: 334.615 0.072 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalAngleWorks (7 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -352387083 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 20 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 186.5 45: (ns/day) (hour/ns) 45: Performance: 314.300 0.076 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (12 ms) 45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to 1288962038 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 19 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 184.9 45: (ns/day) (hour/ns) 45: Performance: 296.553 0.081 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (14 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -942735925 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 23 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 187.1 45: (ns/day) (hour/ns) 45: Performance: 315.120 0.076 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (15 ms) 45: [----------] 6 tests from BondedInteractionsTest (111 ms total) 45: 45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: NVE simulation: will use the initial temperature of 68.810 K for 45: determining the Verlet buffer size 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.019 0.010 199.1 45: (ns/day) (hour/ns) 45: Performance: 151.199 0.159 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.007 0.004 197.2 45: (ns/day) (hour/ns) 45: Performance: 389.788 0.062 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 45: 45: 45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (26 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.002 196.7 45: (ns/day) (hour/ns) 45: Performance: 949.829 0.025 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.002 192.9 45: (ns/day) (hour/ns) 45: Performance: 916.891 0.026 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (27 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: NVE simulation: will use the initial temperature of 398.997 K for 45: determining the Verlet buffer size 45: 45: 45: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 4 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.004 0.002 197.2 45: (ns/day) (hour/ns) 45: Performance: 737.796 0.033 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.004 0.002 194.0 45: (ns/day) (hour/ns) 45: Performance: 733.579 0.033 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (657 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.004 0.002 196.6 45: (ns/day) (hour/ns) 45: Performance: 719.864 0.033 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.008 0.004 196.5 45: (ns/day) (hour/ns) 45: Performance: 340.045 0.071 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (832 ms) 45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (1542 ms total) 45: 45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: NVE simulation: will use the initial temperature of 68.810 K for 45: determining the Verlet buffer size 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.001 192.6 45: (ns/day) (hour/ns) 45: Performance: 1062.171 0.023 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.010 0.005 198.9 45: (ns/day) (hour/ns) 45: Performance: 287.905 0.083 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (23 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: NVE simulation: will use the initial temperature of 68.810 K for 45: determining the Verlet buffer size 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.002 192.0 45: (ns/day) (hour/ns) 45: Performance: 934.698 0.026 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.008 0.004 198.6 45: (ns/day) (hour/ns) 45: Performance: 364.360 0.066 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (21 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.002 192.1 45: (ns/day) (hour/ns) 45: Performance: 939.831 0.026 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.002 196.7 45: (ns/day) (hour/ns) 45: Performance: 963.798 0.025 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (16 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.001 191.5 45: (ns/day) (hour/ns) 45: Performance: 1061.622 0.023 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.004 0.002 195.9 45: (ns/day) (hour/ns) 45: Performance: 821.632 0.029 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (17 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 45: NVE simulation: will use the initial temperature of 398.997 K for 45: determining the Verlet buffer size 45: 45: 45: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 4 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.002 192.8 45: (ns/day) (hour/ns) 45: Performance: 894.655 0.027 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.002 197.4 45: (ns/day) (hour/ns) 45: Performance: 882.733 0.027 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (858 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 45: NVE simulation: will use the initial temperature of 398.997 K for 45: determining the Verlet buffer size 45: 45: 45: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 4 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.002 192.9 45: (ns/day) (hour/ns) 45: Performance: 886.672 0.027 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.005 0.002 197.0 45: (ns/day) (hour/ns) 45: Performance: 603.861 0.040 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (1032 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.020 0.010 198.8 45: (ns/day) (hour/ns) 45: Performance: 149.627 0.160 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.020 0.010 199.2 45: (ns/day) (hour/ns) 45: Performance: 144.710 0.166 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (1340 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 45: 45: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.003 0.002 191.7 45: (ns/day) (hour/ns) 45: Performance: 825.485 0.029 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.004 0.002 196.5 45: (ns/day) (hour/ns) 45: Performance: 659.169 0.036 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 45: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (1353 ms) 45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (4660 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 24 tests from 7 test cases ran. (10485 ms total) 45: [ PASSED ] 24 tests. 45/54 Test #45: MdrunTests .......................... Passed 10.54 sec test 46 Start 46: MdrunNonIntegratorTests 46: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 46: Test timeout computed to be: 600 46: [==========] Running 65 tests from 7 test cases. 46: [----------] Global test environment set-up. 46: [----------] 1 test from NonbondedBenchTest 46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 46: SIMD width: 2 46: System size: 3000 atoms 46: Cut-off radius: 1 nm 46: Number of threads: 1 46: Number of iterations: 1 46: Compute energies: no 46: Ewald excl. corr.: analytical 46: 46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 46: total useful 46: Ewald all geom. 4xM 107.810 107.8099 0.0098 0.0058 46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (105 ms) 46: [----------] 1 test from NonbondedBenchTest (105 ms total) 46: 46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -4.79910463671057e+01 46: Maximum force = 1.86297359432214e+02 on atom 13 46: Norm of force = 8.77219865482122e+01 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1520 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 3.02331e+02 on atom 3 46: F-Norm = 1.18024e+02 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -5.58622538633287e+01 46: Maximum force = 4.27274822366548e+02 on atom 13 46: Norm of force = 1.84530029253846e+02 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1424 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 22.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 3.19376899751522e+02 46: Maximum force = 9.99884921009767e+03 on atom 9 46: Norm of force = 4.61669565054298e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (497 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: 46: NOTE 3 [file glycine_vacuo.top, line 12]: 46: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 46: 46: Number of degrees of freedom in T-Coupling group System is 22.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 2.41575e+04 on atom 10 46: F-Norm = 1.18451e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 1.51743018140927e+02 46: Maximum force = 7.42089573409110e+03 on atom 9 46: Norm of force = 3.56929298615738e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (352 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -1.56984193848274e+02 46: Maximum force = 4.56923624626478e+02 on atom 17 46: Norm of force = 1.83258377168370e+02 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (52 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: 46: NOTE 4 [file unknown]: 46: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 1.06800e+03 on atom 28 46: F-Norm = 4.26922e+02 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -1.69410778678186e+02 46: Maximum force = 2.18225948474111e+02 on atom 17 46: Norm of force = 7.92068036537837e+01 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (48 ms) 46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3893 ms total) 46: 46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents converged to Fmax < 10 in 1 steps 46: Potential Energy = -9.74257075835447e-01 46: Maximum force = 4.01322929015133e+00 on atom 1 46: Norm of force = 1.63839399694378e+00 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (20 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 4.01323e+00 on atom 1 46: F-Norm = 1.63839e+00 46: 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 46: Potential Energy = -9.90642313893969e-01 46: Maximum force = 2.57812909490791e+00 on atom 1 46: Norm of force = 1.05251679559130e+00 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (23 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: 46: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: 46: There was 1 warning 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Low-Memory BFGS Minimizer: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: Using 10 BFGS correction steps. 46: 46: F-max = 4.01323e+00 on atom 1 46: F-Norm = 1.63839e+00 46: 46: 46: writing lowest energy coordinates. 46: 46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 46: Potential Energy = -9.90642313893969e-01 46: Maximum force = 2.57812909490791e+00 on atom 1 46: Norm of force = 1.05251679559130e+00 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (20 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 3.19395484891518e+02 46: Maximum force = 9.97041707197910e+03 on atom 9 46: Norm of force = 4.62274878665467e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (373 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 2.41672e+04 on atom 10 46: F-Norm = 1.19357e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 1.56258793899480e+02 46: Maximum force = 7.50181017480396e+03 on atom 9 46: Norm of force = 3.61390332564874e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (480 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: 46: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: 46: There was 1 warning 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Low-Memory BFGS Minimizer: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: Using 10 BFGS correction steps. 46: 46: F-max = 2.41672e+04 on atom 10 46: F-Norm = 1.19357e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 5.61116097794204e+02 46: Maximum force = 1.26854826291223e+04 on atom 10 46: Norm of force = 6.06436286976271e+03 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (384 ms) 46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1300 ms total) 46: 46: [----------] 5 tests from NormalModesWorks/NormalModesTest 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 3 of the 3 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 3 of the 3 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 15.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=6), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation '2 scaled waters' 46: 12 steps. 46: 46: Maximum force: 9.96989e-06 46: 46: 46: Writing Hessian... 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 18... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--18 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 6 Atoms 46: Using begin = 7 and end = 18 46: Full matrix storage format, nrow=18, ncols=18 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (58 ms) 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 46: 46: NOTE 3 [file villin.top, line 2452]: 46: System has non-zero total charge: -2.000000 46: Total charge should normally be an integer. See 46: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 46: for discussion on how close it should be to an integer. 46: 46: 46: 46: Number of degrees of freedom in T-Coupling group System is 765.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=256), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 46: 512 steps. 46: 46: Maximum force: 6.97568e-04 46: 46: 46: Writing Hessian... 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 50... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--50 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 256 Atoms 46: Using begin = 7 and end = 50 46: Full matrix storage format, nrow=768, ncols=768 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (6328 ms) 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 15.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=6), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation 'flex spc dimer' 46: 12 steps. 46: 46: Maximum force: 3.36401e-04 46: 46: 46: Writing Hessian... 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 18... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--18 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 6 Atoms 46: Using begin = 7 and end = 18 46: Full matrix storage format, nrow=18, ncols=18 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (956 ms) 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Number of degrees of freedom in T-Coupling group System is 6.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=3), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation '1 TIP5P' 46: 6 steps. 46: 46: Maximum force: 2.42882e-04 46: 46: 46: Writing Hessian... 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 9... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--9 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 3 Atoms 46: There are: 2 VSites 46: Using begin = 7 and end = 9 46: Full matrix storage format, nrow=9, ncols=9 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (596 ms) 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: Generated 6 of the 10 non-bonded parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SW' 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Number of degrees of freedom in T-Coupling group System is 15.00 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=6), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation 'sw dimer' 46: 12 steps. 46: 46: Maximum force: 1.07599e-03 46: The force is probably not small enough to ensure that you are at a minimum. 46: Be aware that negative eigenvalues may occur 46: when the resulting matrix is diagonalized. 46: 46: 46: Writing Hessian... 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 18... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--18 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 6 Atoms 46: There are: 2 Shells 46: There are: 2 VSites 46: 46: NOTE: in the current version shell prediction during the crun is disabled 46: 46: Using begin = 7 and end = 18 46: Full matrix storage format, nrow=18, ncols=18 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (11 ms) 46: [----------] 5 tests from NormalModesWorks/NormalModesTest (7949 ms total) 46: 46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 68.810 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 193.3 46: (ns/day) (hour/ns) 46: Performance: 1088.829 0.022 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 46: 46: trr version: GMX_trn_file (double precision) 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 22 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.5 46: (ns/day) (hour/ns) 46: Performance: 2311.667 0.010 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (23 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 68.810 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 197.6 46: (ns/day) (hour/ns) 46: Performance: 649.578 0.037 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 21 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.9 46: (ns/day) (hour/ns) 46: Performance: 2827.257 0.008 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (22 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 192.5 46: (ns/day) (hour/ns) 46: Performance: 1030.372 0.023 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.020 0.010 199.6 46: (ns/day) (hour/ns) 46: Performance: 149.482 0.161 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (27 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 194.7 46: (ns/day) (hour/ns) 46: Performance: 663.285 0.036 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 21 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 195.0 46: (ns/day) (hour/ns) 46: Performance: 2584.142 0.009 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (25 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: NVE simulation: will use the initial temperature of 398.997 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.7 46: (ns/day) (hour/ns) 46: Performance: 898.963 0.027 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 22 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.9 46: (ns/day) (hour/ns) 46: Performance: 2437.908 0.010 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (589 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: NVE simulation: will use the initial temperature of 398.997 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 197.4 46: (ns/day) (hour/ns) 46: Performance: 730.361 0.033 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 22 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 195.1 46: (ns/day) (hour/ns) 46: Performance: 2472.148 0.010 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (591 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.2 46: (ns/day) (hour/ns) 46: Performance: 917.984 0.026 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 25 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.8 46: (ns/day) (hour/ns) 46: Performance: 2041.960 0.012 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (600 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.4 46: (ns/day) (hour/ns) 46: Performance: 811.566 0.030 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 25 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.5 46: (ns/day) (hour/ns) 46: Performance: 1864.586 0.013 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (1043 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: NVE simulation: will use the initial temperature of 456.887 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 6 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.062 0.031 199.2 46: (ns/day) (hour/ns) 46: Performance: 46.895 0.512 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 195.0 46: (ns/day) (hour/ns) 46: Performance: 1041.873 0.023 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (99 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: NVE simulation: will use the initial temperature of 456.887 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 6 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 6 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.046 0.023 198.9 46: (ns/day) (hour/ns) 46: Performance: 62.996 0.381 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 18 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.7 46: (ns/day) (hour/ns) 46: Performance: 1072.527 0.022 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (97 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 173.1 46: (ns/day) (hour/ns) 46: Performance: 381.792 0.063 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 16 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 192.7 46: (ns/day) (hour/ns) 46: Performance: 1150.867 0.021 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (72 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: NOTE: 40 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.041 0.020 199.0 46: (ns/day) (hour/ns) 46: Performance: 71.740 0.335 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.019 0.009 199.2 46: (ns/day) (hour/ns) 46: Performance: 157.246 0.153 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (82 ms) 46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (3274 ms total) 46: 46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.024 0.012 198.3 46: (ns/day) (hour/ns) 46: Performance: 120.486 0.199 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.7 46: (ns/day) (hour/ns) 46: Performance: 966.065 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (50 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.046 0.023 198.5 46: (ns/day) (hour/ns) 46: Performance: 63.195 0.380 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.4 46: (ns/day) (hour/ns) 46: Performance: 984.278 0.024 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (93 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.024 0.012 198.3 46: (ns/day) (hour/ns) 46: Performance: 118.884 0.202 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.2 46: (ns/day) (hour/ns) 46: Performance: 905.171 0.027 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (72 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.047 0.024 198.5 46: (ns/day) (hour/ns) 46: Performance: 61.761 0.389 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.7 46: (ns/day) (hour/ns) 46: Performance: 976.322 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (112 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.118 0.059 199.5 46: (ns/day) (hour/ns) 46: Performance: 24.802 0.968 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.0 46: (ns/day) (hour/ns) 46: Performance: 936.688 0.026 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (143 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.047 0.023 198.9 46: (ns/day) (hour/ns) 46: Performance: 62.666 0.383 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.9 46: (ns/day) (hour/ns) 46: Performance: 987.433 0.024 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (124 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.031 0.015 198.5 46: (ns/day) (hour/ns) 46: Performance: 94.837 0.253 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.9 46: (ns/day) (hour/ns) 46: Performance: 921.004 0.026 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (96 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.016 0.008 197.3 46: (ns/day) (hour/ns) 46: Performance: 179.051 0.134 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.0 46: (ns/day) (hour/ns) 46: Performance: 904.374 0.027 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (88 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.016 0.008 197.5 46: (ns/day) (hour/ns) 46: Performance: 180.245 0.133 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.9 46: (ns/day) (hour/ns) 46: Performance: 948.221 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (85 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.030 0.015 198.4 46: (ns/day) (hour/ns) 46: Performance: 95.852 0.250 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.2 46: (ns/day) (hour/ns) 46: Performance: 941.843 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (91 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.030 0.015 197.9 46: (ns/day) (hour/ns) 46: Performance: 96.764 0.248 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.3 46: (ns/day) (hour/ns) 46: Performance: 929.200 0.026 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (96 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.024 0.012 199.2 46: (ns/day) (hour/ns) 46: Performance: 123.399 0.194 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 195.1 46: (ns/day) (hour/ns) 46: Performance: 995.089 0.024 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (83 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.031 0.016 199.3 46: (ns/day) (hour/ns) 46: Performance: 94.501 0.254 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.0 46: (ns/day) (hour/ns) 46: Performance: 842.993 0.028 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (91 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.029 0.015 199.3 46: (ns/day) (hour/ns) 46: Performance: 100.162 0.240 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.3 46: (ns/day) (hour/ns) 46: Performance: 904.905 0.027 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (100 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.026 0.013 199.3 46: (ns/day) (hour/ns) 46: Performance: 112.393 0.214 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 195.0 46: (ns/day) (hour/ns) 46: Performance: 992.843 0.024 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (96 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: NOTE: 42 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.137 0.069 199.8 46: (ns/day) (hour/ns) 46: Performance: 21.412 1.121 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 54 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.115 0.058 199.8 46: (ns/day) (hour/ns) 46: Performance: 25.543 0.940 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (224 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.022 0.011 199.1 46: (ns/day) (hour/ns) 46: Performance: 135.133 0.178 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.8 46: (ns/day) (hour/ns) 46: Performance: 989.018 0.024 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (106 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.024 0.012 199.1 46: (ns/day) (hour/ns) 46: Performance: 124.035 0.193 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 193.6 46: (ns/day) (hour/ns) 46: Performance: 923.212 0.026 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (60 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.024 0.012 199.1 46: (ns/day) (hour/ns) 46: Performance: 124.233 0.193 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.0 46: (ns/day) (hour/ns) 46: Performance: 908.508 0.026 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (62 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 198.3 46: (ns/day) (hour/ns) 46: Performance: 213.376 0.112 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.4 46: (ns/day) (hour/ns) 46: Performance: 858.739 0.028 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (49 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.017 0.009 198.8 46: (ns/day) (hour/ns) 46: Performance: 171.920 0.140 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.1 46: (ns/day) (hour/ns) 46: Performance: 965.459 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (54 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.015 0.007 198.7 46: (ns/day) (hour/ns) 46: Performance: 199.870 0.120 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 198.4 46: (ns/day) (hour/ns) 46: Performance: 260.998 0.092 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (56 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.021 0.011 197.6 46: (ns/day) (hour/ns) 46: Performance: 135.314 0.177 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 198.4 46: (ns/day) (hour/ns) 46: Performance: 265.097 0.091 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (73 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.017 0.009 197.6 46: (ns/day) (hour/ns) 46: Performance: 168.400 0.143 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.0 46: (ns/day) (hour/ns) 46: Performance: 948.367 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (69 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.090 0.045 199.5 46: (ns/day) (hour/ns) 46: Performance: 32.678 0.734 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.7 46: (ns/day) (hour/ns) 46: Performance: 883.746 0.027 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (160 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.088 0.044 199.4 46: (ns/day) (hour/ns) 46: Performance: 33.147 0.724 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 194.4 46: (ns/day) (hour/ns) 46: Performance: 759.255 0.032 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (155 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.025 0.013 198.1 46: (ns/day) (hour/ns) 46: Performance: 115.688 0.207 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.7 46: (ns/day) (hour/ns) 46: Performance: 917.164 0.026 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (118 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.047 0.023 198.9 46: (ns/day) (hour/ns) 46: Performance: 62.680 0.383 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.9 46: (ns/day) (hour/ns) 46: Performance: 852.206 0.028 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (151 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.090 0.045 199.5 46: (ns/day) (hour/ns) 46: Performance: 32.535 0.738 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.8 46: (ns/day) (hour/ns) 46: Performance: 877.828 0.027 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (152 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.058 0.029 199.2 46: (ns/day) (hour/ns) 46: Performance: 50.652 0.474 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 18 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 195.3 46: (ns/day) (hour/ns) 46: Performance: 954.539 0.025 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (133 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.048 0.024 199.0 46: (ns/day) (hour/ns) 46: Performance: 60.971 0.394 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 190.7 46: (ns/day) (hour/ns) 46: Performance: 882.227 0.027 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (192 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.103 0.051 199.5 46: (ns/day) (hour/ns) 46: Performance: 28.558 0.840 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.9 46: (ns/day) (hour/ns) 46: Performance: 829.151 0.029 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (192 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.032 0.016 198.2 46: (ns/day) (hour/ns) 46: Performance: 89.924 0.267 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 38 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.044 0.022 199.4 46: (ns/day) (hour/ns) 46: Performance: 67.200 0.357 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (150 ms) 46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (3577 ms total) 46: 46: [----------] 2 tests from Angles1/SimpleMdrunTest 46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: Generated 3 of the 3 non-bonded parameter combinations 46: Excluding 3 bonded neighbours molecule type 'butane' 46: 46: NOTE 2 [file angles1.top, line 72]: 46: In moleculetype 'butane' 4 atoms are not bound by a potential or 46: constraint to any other atom in the same moleculetype. Although 46: technically this might not cause issues in a simulation, this often means 46: that the user forgot to add a bond/potential/constraint or put multiple 46: molecules in the same moleculetype definition by mistake. Run with -v to 46: get information for each atom. 46: 46: Number of degrees of freedom in T-Coupling group System is 9.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 238.919 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'This_incredible_box_of_butane' 46: 50 steps, 0.1 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.030 0.015 198.9 46: (ns/day) (hour/ns) 46: Performance: 287.574 0.083 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (33 ms) 46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: Generated 3 of the 3 non-bonded parameter combinations 46: Excluding 3 bonded neighbours molecule type 'butane' 46: 46: NOTE 2 [file angles1.top, line 72]: 46: In moleculetype 'butane' 4 atoms are not bound by a potential or 46: constraint to any other atom in the same moleculetype. Although 46: technically this might not cause issues in a simulation, this often means 46: that the user forgot to add a bond/potential/constraint or put multiple 46: molecules in the same moleculetype definition by mistake. Run with -v to 46: get information for each atom. 46: 46: Number of degrees of freedom in T-Coupling group System is 9.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 238.919 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'This_incredible_box_of_butane' 46: 50 steps, 0.1 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.023 0.012 199.2 46: (ns/day) (hour/ns) 46: Performance: 373.770 0.064 46: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (31 ms) 46: [----------] 2 tests from Angles1/SimpleMdrunTest (64 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 65 tests from 7 test cases ran. (20162 ms total) 46: [ PASSED ] 65 tests. 46/54 Test #46: MdrunNonIntegratorTests ............. Passed 20.27 sec test 47 Start 47: MdrunTpiTests 47: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 47: Test timeout computed to be: 600 47: [==========] Running 2 tests from 1 test case. 47: [----------] Global test environment set-up. 47: [----------] 2 tests from Simple/TpiTest 47: [ RUN ] Simple/TpiTest.ReproducesOutput/0 47: Ignoring obsolete mdp entry 'ns_type' 47: Generated 331705 of the 331705 non-bonded parameter combinations 47: Generating 1-4 interactions: fudge = 0.5 47: Generated 331705 of the 331705 1-4 parameter combinations 47: Excluding 2 bonded neighbours molecule type 'SOL' 47: Excluding 3 bonded neighbours molecule type 'methane' 47: Number of degrees of freedom in T-Coupling group System is 1308.00 47: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 47: log). 47: The current CPU can measure timings more accurately than the code in 47: mdrun-tpi-test was configured to use. This might affect your simulation 47: speed as accurate timings are needed for load-balancing. 47: Please consider rebuilding mdrun-tpi-test with the GMX_USE_RDTSCP=ON CMake option. 47: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 47: 47: TPI is not implemented for GPUs. 47: 47: Using 1 MPI thread 47: 47: Non-default thread affinity set, disabling internal thread affinity 47: 47: Using 1 OpenMP thread 47: 47: Reading frames from gro file '216 water molecules', 648 atoms. 47: Reading frame 0 time 0.000 mu 8.706e+02 8.706e+02 47: Last frame 0 time 0.000 47: Analysing residue names: 47: There are: 216 Water residues 47: There are: 1 Other residues 47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 47: This run will generate roughly 0 Mb of data 47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1826 ms) 47: [ RUN ] Simple/TpiTest.ReproducesOutput/1 47: Ignoring obsolete mdp entry 'ns_type' 47: Generated 331705 of the 331705 non-bonded parameter combinations 47: Generating 1-4 interactions: fudge = 0.5 47: Generated 331705 of the 331705 1-4 parameter combinations 47: Excluding 2 bonded neighbours molecule type 'SOL' 47: Excluding 3 bonded neighbours molecule type 'methane' 47: Number of degrees of freedom in T-Coupling group System is 1308.00 47: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 47: log). 47: The current CPU can measure timings more accurately than the code in 47: mdrun-tpi-test was configured to use. This might affect your simulation 47: speed as accurate timings are needed for load-balancing. 47: Please consider rebuilding mdrun-tpi-test with the GMX_USE_RDTSCP=ON CMake option. 47: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 47: 47: TPI is not implemented for GPUs. 47: 47: Using 1 MPI thread 47: 47: Non-default thread affinity set, disabling internal thread affinity 47: 47: Using 1 OpenMP thread 47: 47: Reading frames from gro file '216 water molecules', 648 atoms. 47: Reading frame 0 time 0.000 mu 9.144e+01 9.144e+01 47: Last frame 0 time 0.000 47: Analysing residue names: 47: There are: 216 Water residues 47: There are: 1 Other residues 47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 47: This run will generate roughly 0 Mb of data 47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (1528 ms) 47: [----------] 2 tests from Simple/TpiTest (3354 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 2 tests from 1 test case ran. (3354 ms total) 47: [ PASSED ] 2 tests. 47/54 Test #47: MdrunTpiTests ....................... Passed 3.41 sec test 48 Start 48: MdrunMpiTests 48: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 48: Test timeout computed to be: 600 48: [==========] Running 22 tests from 7 test cases. 48: [----------] Global test environment set-up. 48: [----------] 1 test from DomainDecompositionSpecialCasesTest 48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -268582945 48: Generated 3 of the 3 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 3 of the 3 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 9.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc2' 48: 0 steps, 0.0 ps. 48: 48: NOTE: 39 % of the run time was spent communicating energies, 48: you might want to increase some nst* mdp options 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.183 0.066 278.7 48: (ns/day) (hour/ns) 48: Performance: 1.316 18.243 48: This run will generate roughly 0 Mb of data 48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (391 ms) 48: [----------] 1 test from DomainDecompositionSpecialCasesTest (391 ms total) 48: 48: [----------] 4 tests from MimicTest 48: [ RUN ] MimicTest.OneQuantumMol 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -153362977 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 53 % of the run time was spent in domain decomposition, 48: 10 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: NOTE: 8 % of the run time was spent communicating energies, 48: you might want to increase some nst* mdp options 48: 48: Core t (s) Wall t (s) (%) 48: Time: 1.197 0.299 399.9 48: (ns/day) (hour/ns) 48: Performance: 0.289 83.148 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.OneQuantumMol (620 ms) 48: [ RUN ] MimicTest.AllQuantumMol 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -1961361541 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 72 % of the run time was spent in domain decomposition, 48: 15 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.500 0.125 399.8 48: (ns/day) (hour/ns) 48: Performance: 0.692 34.702 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.AllQuantumMol (352 ms) 48: [ RUN ] MimicTest.TwoQuantumMol 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -276455463 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 95 % of the run time was spent in domain decomposition, 48: 0 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.498 0.124 399.9 48: (ns/day) (hour/ns) 48: Performance: 0.694 34.569 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.TwoQuantumMol (325 ms) 48: [ RUN ] MimicTest.BondCuts 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -67306771 48: Generated 2211 of the 2211 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2211 of the 2211 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 48: Number of degrees of freedom in T-Coupling group rest is 66.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: NVE simulation: will use the initial temperature of 300.368 K for 48: determining the Verlet buffer size 48: 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase/ala.gro' 48: 48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 19 % of the run time was spent communicating energies, 48: you might want to increase some nst* mdp options 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.042 0.011 398.6 48: (ns/day) (hour/ns) 48: Performance: 8.202 2.926 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.BondCuts (147 ms) 48: [----------] 4 tests from MimicTest (1444 ms total) 48: 48: [----------] 1 test from MultiSimTerminationTest 48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 48: [----------] 1 test from MultiSimTerminationTest (0 ms total) 48: 48: [----------] 3 tests from PmeTest 48: [ RUN ] PmeTest.ReproducesEnergies 48: Setting the LD random seed to -824988161 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 12.00 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 48: NVE simulation: will use the initial temperature of 1046.791 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 48: This run will generate roughly 0 Mb of data 48: 48: Writing final coordinates. 48: 48: NOTE: 10 % of the run time was spent in domain decomposition, 48: 4 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 2.321 0.580 400.0 48: (ns/day) (hour/ns) 48: Performance: 3.126 7.677 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 1.944 0.486 399.9 48: (ns/day) (hour/ns) 48: Performance: 3.733 6.429 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 5.950 1.488 400.0 48: (ns/day) (hour/ns) 48: Performance: 1.220 19.678 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (3624 ms) 48: [ RUN ] PmeTest.ScalesTheBox 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to 600505279 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 12.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: NVE simulation: will use the initial temperature of 1046.791 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 0 steps, 0.0 ps. 48: 48: NOTE: 23 % of the run time was spent in domain decomposition, 48: 30 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.105 0.026 398.7 48: (ns/day) (hour/ns) 48: Performance: 3.291 7.292 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 48: This run will generate roughly 0 Mb of data 48: [ OK ] PmeTest.ScalesTheBox (176 ms) 48: [ RUN ] PmeTest.ScalesTheBoxWithWalls 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -1073762306 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Searching the wall atom type(s) 48: Number of degrees of freedom in T-Coupling group rest is 13.00 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: NVE simulation: will use the initial temperature of 966.268 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 0 steps, 0.0 ps. 48: 48: NOTE: 14 % of the run time was spent in domain decomposition, 48: 14 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.096 0.028 342.3 48: (ns/day) (hour/ns) 48: Performance: 3.072 7.812 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 48: This run will generate roughly 0 Mb of data 48: [ OK ] PmeTest.ScalesTheBoxWithWalls (1468 ms) 48: [----------] 3 tests from PmeTest (5268 ms total) 48: 48: [----------] 1 test from ReplicaExchangeTerminationTest 48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 48: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total) 48: 48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 330891 of the 330891 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 330891 of the 330891 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -4.79910463671059e+01 48: Maximum force = 1.86297359432215e+02 on atom 13 48: Norm of force = 8.77219865482122e+01 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1730 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 330891 of the 330891 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 330891 of the 330891 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 3.02331e+02 on atom 3 48: F-Norm = 1.18024e+02 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -5.58622538633295e+01 48: Maximum force = 4.27274822366511e+02 on atom 13 48: Norm of force = 1.84530029253833e+02 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1062 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 22.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 3.19376899751522e+02 48: Maximum force = 9.99884921009767e+03 on atom 9 48: Norm of force = 4.61669565054298e+03 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1292 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: 48: NOTE 3 [file glycine_vacuo.top, line 12]: 48: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 48: 48: Number of degrees of freedom in T-Coupling group System is 22.00 48: 48: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 4 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 2.41575e+04 on atom 10 48: F-Norm = 1.18451e+04 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 1.51743018140927e+02 48: Maximum force = 7.42089573409110e+03 on atom 9 48: Norm of force = 3.56929298615739e+03 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1952 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 2145 of the 2145 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2145 of the 2145 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 48: 48: NOTE 3 [file unknown]: 48: You are using constraints on all bonds, whereas the forcefield has been 48: parametrized only with constraints involving hydrogen atoms. We suggest 48: using constraints = h-bonds instead, this will also improve performance. 48: 48: Cleaning up constraints and constant bonded interactions with virtual sites 48: Removed 18 Angles with virtual sites, 21 left 48: Removed 10 Proper Dih.s with virtual sites, 44 left 48: Converted 15 Constraints with virtual sites to connections, 7 left 48: Number of degrees of freedom in T-Coupling group System is 23.00 48: 48: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 4 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -1.56984193848274e+02 48: Maximum force = 4.56923624626478e+02 on atom 17 48: Norm of force = 1.83258377168370e+02 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (212 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 2145 of the 2145 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2145 of the 2145 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 48: 48: NOTE 3 [file unknown]: 48: You are using constraints on all bonds, whereas the forcefield has been 48: parametrized only with constraints involving hydrogen atoms. We suggest 48: using constraints = h-bonds instead, this will also improve performance. 48: 48: 48: NOTE 4 [file unknown]: 48: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 48: 48: Cleaning up constraints and constant bonded interactions with virtual sites 48: Removed 18 Angles with virtual sites, 21 left 48: Removed 10 Proper Dih.s with virtual sites, 44 left 48: Converted 15 Constraints with virtual sites to connections, 7 left 48: Number of degrees of freedom in T-Coupling group System is 23.00 48: 48: NOTE 5 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 5 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 1.06800e+03 on atom 28 48: F-Norm = 4.26922e+02 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -1.69410778678186e+02 48: Maximum force = 2.18225948474111e+02 on atom 17 48: Norm of force = 7.92068036537837e+01 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (1027 ms) 48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (7275 ms total) 48: 48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents converged to Fmax < 10 in 1 steps 48: Potential Energy = -9.74257075835447e-01 48: Maximum force = 4.01322929015133e+00 on atom 3 48: Norm of force = 1.63839399694378e+00 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1165 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 4.01323e+00 on atom 3 48: F-Norm = 1.63839e+00 48: 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 48: Potential Energy = -9.90642313893969e-01 48: Maximum force = 2.57812909490791e+00 on atom 3 48: Norm of force = 1.05251679559130e+00 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (76 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: 48: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: 48: There was 1 warning 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (6 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 3.19395484891519e+02 48: Maximum force = 9.97041707197911e+03 on atom 9 48: Norm of force = 4.62274878665467e+03 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1314 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 2.41672e+04 on atom 10 48: F-Norm = 1.19357e+04 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 1.56258793899480e+02 48: Maximum force = 7.50181017480397e+03 on atom 9 48: Norm of force = 3.61390332564874e+03 48: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (885 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 48: 48: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: 48: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: 48: There was 1 warning 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (346 ms) 48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3792 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 22 tests from 7 test cases ran. (18170 ms total) 48: [ PASSED ] 22 tests. 48: 48: YOU HAVE 4 DISABLED TESTS 48: 48/54 Test #48: MdrunMpiTests ....................... Passed 18.24 sec test 49 Start 49: MdrunMpiCoordinationTestsOneRank 49: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml" 49: Test timeout computed to be: 960 49: [==========] Running 27 tests from 3 test cases. 49: [----------] Global test environment set-up. 49: [----------] 1 test from BasicPropagators/PeriodicActionsTest 49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.8 49: (ns/day) (hour/ns) 49: Performance: 473.273 0.051 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.3 49: (ns/day) (hour/ns) 49: Performance: 146.873 0.163 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.6 49: (ns/day) (hour/ns) 49: Performance: 781.702 0.031 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.5 49: (ns/day) (hour/ns) 49: Performance: 994.928 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.7 49: (ns/day) (hour/ns) 49: Performance: 1015.594 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.2 49: (ns/day) (hour/ns) 49: Performance: 958.251 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (305 ms) 49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (305 ms total) 49: 49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1131.007 0.021 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.3 49: (ns/day) (hour/ns) 49: Performance: 1095.022 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.3 49: (ns/day) (hour/ns) 49: Performance: 1071.780 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.6 49: (ns/day) (hour/ns) 49: Performance: 963.496 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.3 49: (ns/day) (hour/ns) 49: Performance: 925.431 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1083.848 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (94 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1067.324 0.022 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1087.292 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 993.804 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.3 49: (ns/day) (hour/ns) 49: Performance: 948.367 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.3 49: (ns/day) (hour/ns) 49: Performance: 151.459 0.158 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.2 49: (ns/day) (hour/ns) 49: Performance: 152.260 0.158 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (100 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1031.925 0.023 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1047.186 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1094.438 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.5 49: (ns/day) (hour/ns) 49: Performance: 931.588 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 995.571 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1058.339 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (92 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.4 49: (ns/day) (hour/ns) 49: Performance: 1157.136 0.021 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.0 49: (ns/day) (hour/ns) 49: Performance: 951.002 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1076.650 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.7 49: (ns/day) (hour/ns) 49: Performance: 915.665 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1007.786 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.3 49: (ns/day) (hour/ns) 49: Performance: 897.653 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (96 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 94.4 49: (ns/day) (hour/ns) 49: Performance: 1038.711 0.023 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1056.524 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1025.228 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.4 49: (ns/day) (hour/ns) 49: Performance: 878.955 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.4 49: (ns/day) (hour/ns) 49: Performance: 942.996 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 994.767 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (96 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.2 49: (ns/day) (hour/ns) 49: Performance: 150.178 0.160 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.2 49: (ns/day) (hour/ns) 49: Performance: 151.728 0.158 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.3 49: (ns/day) (hour/ns) 49: Performance: 145.820 0.165 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.8 49: (ns/day) (hour/ns) 49: Performance: 253.533 0.095 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.8 49: (ns/day) (hour/ns) 49: Performance: 256.062 0.094 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 95.8 49: (ns/day) (hour/ns) 49: Performance: 888.462 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (98 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1099.517 0.022 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1053.994 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1002.538 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1083.086 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1065.478 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.2 49: (ns/day) (hour/ns) 49: Performance: 947.784 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (95 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1015.594 0.024 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.2 49: (ns/day) (hour/ns) 49: Performance: 1024.887 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 986.642 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1046.830 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1014.256 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 95.6 49: (ns/day) (hour/ns) 49: Performance: 974.623 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (110 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.6 49: (ns/day) (hour/ns) 49: Performance: 1048.969 0.023 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1043.108 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1051.834 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1083.658 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.5 49: (ns/day) (hour/ns) 49: Performance: 1036.090 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1060.343 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (92 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.006 26.2 49: (ns/day) (hour/ns) 49: Performance: 261.275 0.092 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.3 49: (ns/day) (hour/ns) 49: Performance: 999.772 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.3 49: (ns/day) (hour/ns) 49: Performance: 992.843 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 986.484 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1077.027 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.5 49: (ns/day) (hour/ns) 49: Performance: 1041.344 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (100 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.4 49: (ns/day) (hour/ns) 49: Performance: 1090.371 0.022 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1005.975 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.4 49: (ns/day) (hour/ns) 49: Performance: 1017.271 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 95.8 49: (ns/day) (hour/ns) 49: Performance: 962.292 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1030.372 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1100.696 0.022 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (101 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.006 24.7 49: (ns/day) (hour/ns) 49: Performance: 265.669 0.090 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.5 49: (ns/day) (hour/ns) 49: Performance: 260.987 0.092 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 95.8 49: (ns/day) (hour/ns) 49: Performance: 947.638 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.0 49: (ns/day) (hour/ns) 49: Performance: 947.638 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.3 49: (ns/day) (hour/ns) 49: Performance: 1023.865 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.9 49: (ns/day) (hour/ns) 49: Performance: 253.418 0.095 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (101 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.1 49: (ns/day) (hour/ns) 49: Performance: 248.091 0.097 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.3 49: (ns/day) (hour/ns) 49: Performance: 249.467 0.096 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.4 49: (ns/day) (hour/ns) 49: Performance: 252.514 0.095 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 922.383 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.6 49: (ns/day) (hour/ns) 49: Performance: 855.400 0.028 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 881.975 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (97 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 95.5 49: (ns/day) (hour/ns) 49: Performance: 971.243 0.025 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1008.776 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1012.423 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1043.108 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 95.6 49: (ns/day) (hour/ns) 49: Performance: 907.571 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1007.951 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (96 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.1 49: (ns/day) (hour/ns) 49: Performance: 993.164 0.024 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.0 49: (ns/day) (hour/ns) 49: Performance: 859.698 0.028 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 879.833 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.5 49: (ns/day) (hour/ns) 49: Performance: 897.915 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.5 49: (ns/day) (hour/ns) 49: Performance: 937.828 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 98.5 49: (ns/day) (hour/ns) 49: Performance: 1010.265 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (97 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1066.954 0.022 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.6 49: (ns/day) (hour/ns) 49: Performance: 900.803 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 95.7 49: (ns/day) (hour/ns) 49: Performance: 905.171 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.0 49: (ns/day) (hour/ns) 49: Performance: 887.055 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.8 49: (ns/day) (hour/ns) 49: Performance: 261.153 0.092 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.6 49: (ns/day) (hour/ns) 49: Performance: 247.971 0.097 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (102 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.8 49: (ns/day) (hour/ns) 49: Performance: 248.141 0.097 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.9 49: (ns/day) (hour/ns) 49: Performance: 245.628 0.098 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.5 49: (ns/day) (hour/ns) 49: Performance: 904.772 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.4 49: (ns/day) (hour/ns) 49: Performance: 905.570 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 93.4 49: (ns/day) (hour/ns) 49: Performance: 799.247 0.030 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.5 49: (ns/day) (hour/ns) 49: Performance: 869.649 0.028 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (103 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.7 49: (ns/day) (hour/ns) 49: Performance: 244.575 0.098 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.8 49: (ns/day) (hour/ns) 49: Performance: 243.021 0.099 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.0 49: (ns/day) (hour/ns) 49: Performance: 237.769 0.101 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.8 49: (ns/day) (hour/ns) 49: Performance: 763.678 0.031 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 95.8 49: (ns/day) (hour/ns) 49: Performance: 788.203 0.030 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.8 49: (ns/day) (hour/ns) 49: Performance: 248.211 0.097 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (108 ms) 49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (1778 ms total) 49: 49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1013.589 0.024 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.1 49: (ns/day) (hour/ns) 49: Performance: 876.329 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.4 49: (ns/day) (hour/ns) 49: Performance: 151.832 0.158 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.3 49: (ns/day) (hour/ns) 49: Performance: 148.659 0.161 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.3 49: (ns/day) (hour/ns) 49: Performance: 149.319 0.161 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1048.433 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (8714 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1068.620 0.022 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 97.1 49: (ns/day) (hour/ns) 49: Performance: 664.860 0.036 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.3 49: (ns/day) (hour/ns) 49: Performance: 147.091 0.163 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1049.326 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.2 49: (ns/day) (hour/ns) 49: Performance: 150.479 0.159 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.0 49: (ns/day) (hour/ns) 49: Performance: 1037.486 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (7817 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.0 49: (ns/day) (hour/ns) 49: Performance: 436.241 0.055 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.1 49: (ns/day) (hour/ns) 49: Performance: 1134.130 0.021 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.1 49: (ns/day) (hour/ns) 49: Performance: 947.784 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.1 49: (ns/day) (hour/ns) 49: Performance: 899.619 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 452.353 0.053 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.3 49: (ns/day) (hour/ns) 49: Performance: 460.571 0.052 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (6160 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.9 49: (ns/day) (hour/ns) 49: Performance: 1045.231 0.023 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.8 49: (ns/day) (hour/ns) 49: Performance: 1064.925 0.023 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 96.2 49: (ns/day) (hour/ns) 49: Performance: 1017.943 0.024 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 95.8 49: (ns/day) (hour/ns) 49: Performance: 899.751 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.7 49: (ns/day) (hour/ns) 49: Performance: 254.949 0.094 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 95.5 49: (ns/day) (hour/ns) 49: Performance: 918.532 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (6723 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 95.8 49: (ns/day) (hour/ns) 49: Performance: 966.823 0.025 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 95.9 49: (ns/day) (hour/ns) 49: Performance: 791.850 0.030 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: NOTE: 84 % of the run time was spent in pair search, 49: you might want to increase nstlist (this has no effect on accuracy) 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.2 49: (ns/day) (hour/ns) 49: Performance: 152.324 0.158 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.013 0.013 99.3 49: (ns/day) (hour/ns) 49: Performance: 116.501 0.206 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.5 49: (ns/day) (hour/ns) 49: Performance: 399.805 0.060 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 97.0 49: (ns/day) (hour/ns) 49: Performance: 823.609 0.029 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (7777 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.001 95.7 49: (ns/day) (hour/ns) 49: Performance: 1010.762 0.024 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.001 0.002 96.1 49: (ns/day) (hour/ns) 49: Performance: 948.075 0.025 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.2 49: (ns/day) (hour/ns) 49: Performance: 145.986 0.164 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.2 49: (ns/day) (hour/ns) 49: Performance: 147.432 0.163 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.0 49: (ns/day) (hour/ns) 49: Performance: 873.100 0.027 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 96.5 49: (ns/day) (hour/ns) 49: Performance: 813.817 0.029 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (8198 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.6 49: (ns/day) (hour/ns) 49: Performance: 144.829 0.166 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.8 49: (ns/day) (hour/ns) 49: Performance: 916.210 0.026 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.5 49: (ns/day) (hour/ns) 49: Performance: 243.704 0.098 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 831.951 0.029 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.014 0.014 99.8 49: (ns/day) (hour/ns) 49: Performance: 104.956 0.229 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 771.328 0.031 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (8000 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.8 49: (ns/day) (hour/ns) 49: Performance: 629.017 0.038 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.5 49: (ns/day) (hour/ns) 49: Performance: 145.986 0.164 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 864.402 0.028 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.010 0.010 99.7 49: (ns/day) (hour/ns) 49: Performance: 148.362 0.162 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.6 49: (ns/day) (hour/ns) 49: Performance: 804.360 0.030 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.014 0.014 99.7 49: (ns/day) (hour/ns) 49: Performance: 102.173 0.235 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (9387 ms) 49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (62777 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 27 tests from 3 test cases ran. (64860 ms total) 49: [ PASSED ] 27 tests. 49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 64.93 sec test 50 Start 50: MdrunMpiCoordinationTestsTwoRanks 50: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml" 50: Test timeout computed to be: 960 50: [==========] Running 27 tests from 3 test cases. 50: [----------] Global test environment set-up. 50: [----------] 1 test from BasicPropagators/PeriodicActionsTest 50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 93.0%. 50: The balanceable part of the MD step is 26%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 24.1%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: NOTE: 24.1 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You can consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 28 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 12 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.394 0.223 176.7 50: (ns/day) (hour/ns) 50: Performance: 6.593 3.640 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.5%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.7%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 193.0 50: (ns/day) (hour/ns) 50: Performance: 688.527 0.035 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 4.0%. 50: The balanceable part of the MD step is 46%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.8%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 786.693 0.031 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.0%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 754.512 0.032 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.7%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.8%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 752.761 0.032 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.8%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.6 50: (ns/day) (hour/ns) 50: Performance: 815.919 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (902 ms) 50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (902 ms total) 50: 50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.3%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.7%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 751.292 0.032 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.6%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.6 50: (ns/day) (hour/ns) 50: Performance: 859.098 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.1%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.1 50: (ns/day) (hour/ns) 50: Performance: 803.416 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.9%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.4%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 885.143 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.8%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.9%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.2 50: (ns/day) (hour/ns) 50: Performance: 890.066 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 4.4%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.2%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.3 50: (ns/day) (hour/ns) 50: Performance: 914.510 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (244 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 4.1%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.9%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.1 50: (ns/day) (hour/ns) 50: Performance: 819.337 0.029 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.7%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 805.148 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.5%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.0 50: (ns/day) (hour/ns) 50: Performance: 897.065 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.4%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.7%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 748.781 0.032 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.7%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.8%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.1 50: (ns/day) (hour/ns) 50: Performance: 650.950 0.037 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 4.1%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.9%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 861.863 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (308 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.0%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.2 50: (ns/day) (hour/ns) 50: Performance: 763.300 0.031 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.0%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.6 50: (ns/day) (hour/ns) 50: Performance: 834.995 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.0%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 92 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.043 0.029 145.9 50: (ns/day) (hour/ns) 50: Performance: 50.112 0.479 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.1%. 50: The balanceable part of the MD step is 5%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.1%. 50: 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.020 0.010 198.4 50: (ns/day) (hour/ns) 50: Performance: 145.949 0.164 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.7%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 752.163 0.032 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.6%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.4 50: (ns/day) (hour/ns) 50: Performance: 838.233 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (404 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.2 50: (ns/day) (hour/ns) 50: Performance: 835.278 0.029 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 850.617 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.5 50: (ns/day) (hour/ns) 50: Performance: 857.424 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.4 50: (ns/day) (hour/ns) 50: Performance: 788.758 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.1 50: (ns/day) (hour/ns) 50: Performance: 932.364 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 897.392 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (407 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 190.4 50: (ns/day) (hour/ns) 50: Performance: 986.563 0.024 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.2 50: (ns/day) (hour/ns) 50: Performance: 894.980 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.028 0.014 198.6 50: (ns/day) (hour/ns) 50: Performance: 104.050 0.231 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.4 50: (ns/day) (hour/ns) 50: Performance: 903.578 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 189.7 50: (ns/day) (hour/ns) 50: Performance: 852.088 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 958.623 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (369 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 881.218 0.027 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.1 50: (ns/day) (hour/ns) 50: Performance: 928.639 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 186.7 50: (ns/day) (hour/ns) 50: Performance: 837.208 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 849.854 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.4 50: (ns/day) (hour/ns) 50: Performance: 834.373 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.7 50: (ns/day) (hour/ns) 50: Performance: 965.989 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (400 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 191.2 50: (ns/day) (hour/ns) 50: Performance: 985.853 0.024 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 34 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.5 50: (ns/day) (hour/ns) 50: Performance: 893.811 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.7 50: (ns/day) (hour/ns) 50: Performance: 923.005 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 875.457 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.3 50: (ns/day) (hour/ns) 50: Performance: 972.623 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.2 50: (ns/day) (hour/ns) 50: Performance: 887.630 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (388 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.3 50: (ns/day) (hour/ns) 50: Performance: 935.124 0.026 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.001 187.7 50: (ns/day) (hour/ns) 50: Performance: 1006.962 0.024 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.1 50: (ns/day) (hour/ns) 50: Performance: 845.829 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 946.255 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.5 50: (ns/day) (hour/ns) 50: Performance: 876.828 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.2 50: (ns/day) (hour/ns) 50: Performance: 823.389 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (340 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 189.4 50: (ns/day) (hour/ns) 50: Performance: 787.800 0.030 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 189.6 50: (ns/day) (hour/ns) 50: Performance: 843.570 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 189.4 50: (ns/day) (hour/ns) 50: Performance: 854.096 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 85 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.026 0.013 198.3 50: (ns/day) (hour/ns) 50: Performance: 113.229 0.212 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.2 50: (ns/day) (hour/ns) 50: Performance: 887.566 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 189.8 50: (ns/day) (hour/ns) 50: Performance: 940.764 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1052 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.7 50: (ns/day) (hour/ns) 50: Performance: 841.899 0.029 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 965.535 0.025 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.1 50: (ns/day) (hour/ns) 50: Performance: 910.119 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 188.8 50: (ns/day) (hour/ns) 50: Performance: 846.642 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 919.903 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 33 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.2 50: (ns/day) (hour/ns) 50: Performance: 769.257 0.031 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (608 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.5 50: (ns/day) (hour/ns) 50: Performance: 854.037 0.028 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 189.1 50: (ns/day) (hour/ns) 50: Performance: 914.510 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.9 50: (ns/day) (hour/ns) 50: Performance: 793.124 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.2 50: (ns/day) (hour/ns) 50: Performance: 920.385 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.3 50: (ns/day) (hour/ns) 50: Performance: 850.441 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 188.5 50: (ns/day) (hour/ns) 50: Performance: 891.225 0.027 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (360 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.9 50: (ns/day) (hour/ns) 50: Performance: 790.681 0.030 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 819.664 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.9 50: (ns/day) (hour/ns) 50: Performance: 935.407 0.026 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 787.649 0.030 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 190.5 50: (ns/day) (hour/ns) 50: Performance: 850.734 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 184.4 50: (ns/day) (hour/ns) 50: Performance: 859.518 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (340 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.0%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.7%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.003 190.9 50: (ns/day) (hour/ns) 50: Performance: 558.987 0.043 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.1%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.2 50: (ns/day) (hour/ns) 50: Performance: 648.177 0.037 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.0%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 600.301 0.040 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.4%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.4%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 614.554 0.039 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 4.1%. 50: The balanceable part of the MD step is 56%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.3%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 191.2 50: (ns/day) (hour/ns) 50: Performance: 592.564 0.041 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.7%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 70 % of the run time was spent in domain decomposition, 50: 1 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.027 0.014 198.4 50: (ns/day) (hour/ns) 50: Performance: 107.855 0.223 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (372 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.5%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.1 50: (ns/day) (hour/ns) 50: Performance: 754.143 0.032 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.7%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.2 50: (ns/day) (hour/ns) 50: Performance: 763.158 0.031 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.3%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 189.9 50: (ns/day) (hour/ns) 50: Performance: 676.802 0.035 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.9%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.2 50: (ns/day) (hour/ns) 50: Performance: 647.768 0.037 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.8%. 50: The balanceable part of the MD step is 54%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 709.419 0.034 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.7%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 772.053 0.031 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (288 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.7 50: (ns/day) (hour/ns) 50: Performance: 690.533 0.035 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 190.8 50: (ns/day) (hour/ns) 50: Performance: 615.936 0.039 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 190.4 50: (ns/day) (hour/ns) 50: Performance: 617.758 0.039 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.7 50: (ns/day) (hour/ns) 50: Performance: 767.675 0.031 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.1 50: (ns/day) (hour/ns) 50: Performance: 626.427 0.038 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 191.6 50: (ns/day) (hour/ns) 50: Performance: 619.622 0.039 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (324 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 34 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 767.293 0.031 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 82 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.036 0.018 199.0 50: (ns/day) (hour/ns) 50: Performance: 81.989 0.293 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.7 50: (ns/day) (hour/ns) 50: Performance: 852.147 0.028 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 10 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.017 0.008 197.6 50: (ns/day) (hour/ns) 50: Performance: 173.440 0.138 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.6 50: (ns/day) (hour/ns) 50: Performance: 782.944 0.031 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 33 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.2 50: (ns/day) (hour/ns) 50: Performance: 730.794 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (372 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 739.656 0.032 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 703.585 0.034 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.4 50: (ns/day) (hour/ns) 50: Performance: 683.334 0.035 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 192.3 50: (ns/day) (hour/ns) 50: Performance: 827.036 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 91 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.036 0.018 198.2 50: (ns/day) (hour/ns) 50: Performance: 80.687 0.297 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 31 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.4 50: (ns/day) (hour/ns) 50: Performance: 661.327 0.036 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (320 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 192.6 50: (ns/day) (hour/ns) 50: Performance: 628.279 0.038 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 626.108 0.038 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.1 50: (ns/day) (hour/ns) 50: Performance: 648.484 0.037 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 595.773 0.040 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 91 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.037 0.019 198.4 50: (ns/day) (hour/ns) 50: Performance: 78.911 0.304 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 614.799 0.039 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (348 ms) 50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (7244 ms total) 50: 50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 5.2%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.6%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 831.557 0.029 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.1%. 50: The balanceable part of the MD step is 37%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.0%. 50: 50: 50: NOTE: 18 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 12 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 1.520 0.776 195.9 50: (ns/day) (hour/ns) 50: Performance: 1.893 12.676 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 6.1%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.9%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.9 50: (ns/day) (hour/ns) 50: Performance: 726.656 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 7.6%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.9%. 50: 50: 50: NOTE: 27 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.4 50: (ns/day) (hour/ns) 50: Performance: 678.891 0.035 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 7.3%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.6%. 50: 50: 50: NOTE: 27 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.9 50: (ns/day) (hour/ns) 50: Performance: 695.876 0.034 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 4.9%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.4%. 50: 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.2 50: (ns/day) (hour/ns) 50: Performance: 730.101 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (10552 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 8.3%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 4.0%. 50: 50: 50: NOTE: 77 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.055 0.035 155.1 50: (ns/day) (hour/ns) 50: Performance: 41.748 0.575 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 4.2%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.2%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 831.838 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 4.3%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.3%. 50: 50: 50: NOTE: 29 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.3 50: (ns/day) (hour/ns) 50: Performance: 831.445 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 5.9%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.9%. 50: 50: 50: NOTE: 47 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.037 0.018 199.0 50: (ns/day) (hour/ns) 50: Performance: 79.712 0.301 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 7.1%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.5%. 50: 50: 50: NOTE: 27 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 758.460 0.032 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 9.3%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 4.6%. 50: 50: 50: NOTE: 26 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.6 50: (ns/day) (hour/ns) 50: Performance: 723.626 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (8216 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.3 50: (ns/day) (hour/ns) 50: Performance: 713.569 0.034 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.9 50: (ns/day) (hour/ns) 50: Performance: 688.719 0.035 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 724.776 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.087 1.043 200.0 50: (ns/day) (hour/ns) 50: Performance: 1.408 17.050 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.1 50: (ns/day) (hour/ns) 50: Performance: 756.365 0.032 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.4 50: (ns/day) (hour/ns) 50: Performance: 695.837 0.034 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (9245 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 190.5 50: (ns/day) (hour/ns) 50: Performance: 733.404 0.033 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 194.4 50: (ns/day) (hour/ns) 50: Performance: 461.692 0.052 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 701.542 0.034 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.003 0.002 191.7 50: (ns/day) (hour/ns) 50: Performance: 818.792 0.029 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.1 50: (ns/day) (hour/ns) 50: Performance: 650.366 0.037 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 192.3 50: (ns/day) (hour/ns) 50: Performance: 625.187 0.038 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (9056 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 193.0 50: (ns/day) (hour/ns) 50: Performance: 644.245 0.037 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 192.5 50: (ns/day) (hour/ns) 50: Performance: 620.028 0.039 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.5 50: (ns/day) (hour/ns) 50: Performance: 719.317 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.9 50: (ns/day) (hour/ns) 50: Performance: 778.246 0.031 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 193.9 50: (ns/day) (hour/ns) 50: Performance: 687.221 0.035 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 193.6 50: (ns/day) (hour/ns) 50: Performance: 699.908 0.034 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (8359 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.9 50: (ns/day) (hour/ns) 50: Performance: 708.848 0.034 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 27 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.015 1.024 196.9 50: (ns/day) (hour/ns) 50: Performance: 1.435 16.725 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 28 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 2.092 1.078 194.1 50: (ns/day) (hour/ns) 50: Performance: 1.363 17.611 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.0 50: (ns/day) (hour/ns) 50: Performance: 706.814 0.034 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.8 50: (ns/day) (hour/ns) 50: Performance: 661.718 0.036 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 192.7 50: (ns/day) (hour/ns) 50: Performance: 730.707 0.033 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (9268 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 86.8%. 50: The balanceable part of the MD step is 9%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 7.4%. 50: 50: NOTE: 7.4 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You might want to use dynamic load balancing (option -dlb.) 50: You can also consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 56 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.099 0.050 199.5 50: (ns/day) (hour/ns) 50: Performance: 29.510 0.813 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 8.6%. 50: The balanceable part of the MD step is 55%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 4.7%. 50: 50: 50: NOTE: 78 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.021 0.010 197.5 50: (ns/day) (hour/ns) 50: Performance: 140.579 0.171 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 5.4%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.1%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.004 0.002 191.7 50: (ns/day) (hour/ns) 50: Performance: 663.071 0.036 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.4%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.4%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 191.8 50: (ns/day) (hour/ns) 50: Performance: 603.566 0.040 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.1%. 50: The balanceable part of the MD step is 58%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.6%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 190.9 50: (ns/day) (hour/ns) 50: Performance: 607.733 0.039 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 5.8%. 50: The balanceable part of the MD step is 56%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.2%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.002 191.0 50: (ns/day) (hour/ns) 50: Performance: 596.033 0.040 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (5395 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 191.3 50: (ns/day) (hour/ns) 50: Performance: 491.138 0.049 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 7 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.003 192.3 50: (ns/day) (hour/ns) 50: Performance: 567.587 0.042 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 192.5 50: (ns/day) (hour/ns) 50: Performance: 507.045 0.047 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.003 191.8 50: (ns/day) (hour/ns) 50: Performance: 538.843 0.045 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 34 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 4.401 2.216 198.6 50: (ns/day) (hour/ns) 50: Performance: 0.663 36.209 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: 50: NOTE 1 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 36 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 5.216 2.626 198.6 50: (ns/day) (hour/ns) 50: Performance: 0.559 42.908 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (10962 ms) 50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (71054 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 27 tests from 3 test cases ran. (79200 ms total) 50: [ PASSED ] 27 tests. 50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 79.26 sec test 51 Start 51: GmxapiExternalInterfaceTests 51: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 51: Test timeout computed to be: 600 51: [==========] Running 9 tests from 2 test cases. 51: [----------] Global test environment set-up. 51: [----------] 8 tests from GmxApiTest 51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 51: Setting the LD random seed to -1779223585 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.003 0.002 189.8 51: (ns/day) (hour/ns) 51: Performance: 323.487 0.074 51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (865 ms) 51: [ RUN ] GmxApiTest.SystemConstruction 51: Setting the LD random seed to -162271780 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: [ OK ] GmxApiTest.SystemConstruction (1193 ms) 51: [ RUN ] GmxApiTest.SaneVersionComparisons 51: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 51: [ RUN ] GmxApiTest.VersionNamed0_1_Features 51: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 51: [ RUN ] GmxApiTest.RunnerBasicMD 51: Setting the LD random seed to -1376263 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.006 0.003 194.6 51: (ns/day) (hour/ns) 51: Performance: 178.150 0.135 51: [ OK ] GmxApiTest.RunnerBasicMD (951 ms) 51: [ RUN ] GmxApiTest.RunnerReinitialize 51: Setting the LD random seed to -581964035 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: 51: Received the remote INT/TERM signal, stopping within 50 steps 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.021 0.010 198.4 51: (ns/day) (hour/ns) 51: Performance: 342.439 0.070 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.020 0.010 198.1 51: (ns/day) (hour/ns) 51: Performance: 351.967 0.068 51: [ OK ] GmxApiTest.RunnerReinitialize (994 ms) 51: [ RUN ] GmxApiTest.RunnerContinuedMD 51: Setting the LD random seed to 1738251418 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 10 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.043 0.021 199.0 51: (ns/day) (hour/ns) 51: Performance: 86.405 0.278 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: 51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: Writing final coordinates. 51: 51: NOTE: 80 % of the run time was spent in pair search, 51: you might want to increase nstlist (this has no effect on accuracy) 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.020 0.010 198.5 51: (ns/day) (hour/ns) 51: Performance: 345.504 0.069 51: [ OK ] GmxApiTest.RunnerContinuedMD (1194 ms) 51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 51: Setting the LD random seed to -1052675 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 1, rlist from 1.041 to 1 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 1 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.002 0.001 189.3 51: (ns/day) (hour/ns) 51: Performance: 287.953 0.083 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: 51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps 51: Changing nstlist from 10 to 1, rlist from 1.041 to 1 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.002 0.001 187.8 51: (ns/day) (hour/ns) 51: Performance: 324.376 0.074 51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (1005 ms) 51: [----------] 8 tests from GmxApiTest (6202 ms total) 51: 51: [----------] 1 test from GmxApiBasicTest 51: [ RUN ] GmxApiBasicTest.Status 51: [ OK ] GmxApiBasicTest.Status (0 ms) 51: [----------] 1 test from GmxApiBasicTest (3 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 2 test cases ran. (6205 ms total) 51: [ PASSED ] 9 tests. 51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 6.24 sec test 52 Start 52: GmxapiMpiTests 52: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxapiMpiTests.xml" 52: Test timeout computed to be: 600 52: [==========] Running 9 tests from 2 test cases. 52: [----------] Global test environment set-up. 52: [----------] 8 tests from GmxApiTest 52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 52: Setting the LD random seed to 1060417507 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.002 0.001 190.3 52: (ns/day) (hour/ns) 52: Performance: 387.122 0.062 52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (846 ms) 52: [ RUN ] GmxApiTest.SystemConstruction 52: Setting the LD random seed to 2075912171 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: [ OK ] GmxApiTest.SystemConstruction (939 ms) 52: [ RUN ] GmxApiTest.SaneVersionComparisons 52: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 52: [ RUN ] GmxApiTest.VersionNamed0_1_Features 52: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 52: [ RUN ] GmxApiTest.RunnerBasicMD 52: Setting the LD random seed to -151265417 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.002 0.001 190.1 52: (ns/day) (hour/ns) 52: Performance: 399.956 0.060 52: [ OK ] GmxApiTest.RunnerBasicMD (1097 ms) 52: [ RUN ] GmxApiTest.RunnerReinitialize 52: Setting the LD random seed to -7348241 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: 52: Received the remote INT/TERM signal, stopping within 50 steps 52: 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.004 0.002 193.6 52: (ns/day) (hour/ns) 52: Performance: 1767.158 0.014 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.004 0.002 192.5 52: (ns/day) (hour/ns) 52: Performance: 1828.012 0.013 52: [ OK ] GmxApiTest.RunnerReinitialize (1217 ms) 52: [ RUN ] GmxApiTest.RunnerContinuedMD 52: Setting the LD random seed to -1201143937 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 10 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.003 0.002 192.0 52: (ns/day) (hour/ns) 52: Performance: 1219.561 0.020 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: 52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.028 0.014 199.0 52: (ns/day) (hour/ns) 52: Performance: 248.771 0.096 52: [ OK ] GmxApiTest.RunnerContinuedMD (1086 ms) 52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 52: Setting the LD random seed to -604504961 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 1, rlist from 1.041 to 1 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 1 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.002 0.001 189.7 52: (ns/day) (hour/ns) 52: Performance: 263.363 0.091 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: 52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps 52: Changing nstlist from 10 to 1, rlist from 1.041 to 1 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.002 0.001 188.6 52: (ns/day) (hour/ns) 52: Performance: 298.771 0.080 52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (1277 ms) 52: [----------] 8 tests from GmxApiTest (6462 ms total) 52: 52: [----------] 1 test from GmxApiBasicTest 52: [ RUN ] GmxApiBasicTest.Status 52: [ OK ] GmxApiBasicTest.Status (0 ms) 52: [----------] 1 test from GmxApiBasicTest (0 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 9 tests from 2 test cases ran. (6462 ms total) 52: [ PASSED ] 9 tests. 52/54 Test #52: GmxapiMpiTests ...................... Passed 6.51 sec test 53 Start 53: GmxapiInternalInterfaceTests 53: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 53: Test timeout computed to be: 600 53: [==========] Running 2 tests from 1 test case. 53: [----------] Global test environment set-up. 53: [----------] 2 tests from GmxApiTest 53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 53: Setting the LD random seed to -2088784135 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: Generating 1-4 interactions: fudge = 0.5 53: Generated 331705 of the 331705 1-4 parameter combinations 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: NOTE 1 [file spc_and_methane.top, line 33]: 53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 53: the time step of 2.0e-03 ps. 53: Maybe you forgot to change the constraints mdp option. 53: 53: Number of degrees of freedom in T-Coupling group System is 18.00 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 2 notes 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: This run will generate roughly 0 Mb of data 53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (1085 ms) 53: [ RUN ] GmxApiTest.CreateApiWorkflow 53: Setting the LD random seed to 938470101 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: Generating 1-4 interactions: fudge = 0.5 53: Generated 331705 of the 331705 1-4 parameter combinations 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: NOTE 1 [file spc_and_methane.top, line 33]: 53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 53: the time step of 2.0e-03 ps. 53: Maybe you forgot to change the constraints mdp option. 53: 53: Number of degrees of freedom in T-Coupling group System is 18.00 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 2 notes 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: This run will generate roughly 0 Mb of data 53: [ OK ] GmxApiTest.CreateApiWorkflow (621 ms) 53: [----------] 2 tests from GmxApiTest (1707 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 2 tests from 1 test case ran. (1707 ms total) 53: [ PASSED ] 2 tests. 53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 1.75 sec test 54 Start 54: GmxapiInternalsMpiTests 54: Test command: /build/reproducible-path/gromacs-2020.6/build/basic-dp/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxapiInternalsMpiTests.xml" 54: Test timeout computed to be: 600 54: [==========] Running 2 tests from 1 test case. 54: [----------] Global test environment set-up. 54: [----------] 2 tests from GmxApiTest 54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 54: Setting the LD random seed to -295081217 54: Generated 331705 of the 331705 non-bonded parameter combinations 54: Generating 1-4 interactions: fudge = 0.5 54: Generated 331705 of the 331705 1-4 parameter combinations 54: Excluding 2 bonded neighbours molecule type 'SOL' 54: Excluding 3 bonded neighbours molecule type 'methane' 54: 54: NOTE 1 [file spc_and_methane.top, line 33]: 54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 54: the time step of 2.0e-03 ps. 54: Maybe you forgot to change the constraints mdp option. 54: 54: Number of degrees of freedom in T-Coupling group System is 18.00 54: 54: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 54: You are using a plain Coulomb cut-off, which might produce artifacts. 54: You might want to consider using PME electrostatics. 54: 54: 54: 54: There were 2 notes 54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 54: Note that mdrun will redetermine rlist based on the actual pair-list setup 54: This run will generate roughly 0 Mb of data 54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (709 ms) 54: [ RUN ] GmxApiTest.CreateApiWorkflow 54: Setting the LD random seed to 930796918 54: Generated 331705 of the 331705 non-bonded parameter combinations 54: Generating 1-4 interactions: fudge = 0.5 54: Generated 331705 of the 331705 1-4 parameter combinations 54: Excluding 2 bonded neighbours molecule type 'SOL' 54: Excluding 3 bonded neighbours molecule type 'methane' 54: 54: NOTE 1 [file spc_and_methane.top, line 33]: 54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 54: the time step of 2.0e-03 ps. 54: Maybe you forgot to change the constraints mdp option. 54: 54: Number of degrees of freedom in T-Coupling group System is 18.00 54: 54: NOTE 2 [file /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 54: You are using a plain Coulomb cut-off, which might produce artifacts. 54: You might want to consider using PME electrostatics. 54: 54: 54: 54: There were 2 notes 54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 54: Note that mdrun will redetermine rlist based on the actual pair-list setup 54: This run will generate roughly 0 Mb of data 54: [ OK ] GmxApiTest.CreateApiWorkflow (657 ms) 54: [----------] 2 tests from GmxApiTest (1366 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 2 tests from 1 test case ran. (1367 ms total) 54: [ PASSED ] 2 tests. 54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 1.39 sec 100% tests passed, 0 tests failed out of 54 Label Time Summary: GTest = 242.89 sec*proc (54 tests) IntegrationTest = 76.34 sec*proc (12 tests) MpiTest = 171.48 sec*proc (8 tests) SlowTest = 144.19 sec*proc (2 tests) UnitTest = 22.36 sec*proc (40 tests) Total Test time (real) = 242.97 sec touch build-basic dh_testdir /usr/bin/make -j16 -C build/mpich make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/mpich/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/mpich//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target scanner Scanning dependencies of target release-version-info Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/parser.cpp /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/mpich/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/mpich/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/scanner.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build Scanning dependencies of target modularsimulator Scanning dependencies of target linearalgebra Scanning dependencies of target thread_mpi make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' Scanning dependencies of target tng_io_obj make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' Scanning dependencies of target mdrun_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/matrix.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/mdrun.cpp [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/dict.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c [ 1%] Built target thread_mpi cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/energyelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/propagator.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 2%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/shellfcelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat 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VERSION_VARIABLES=/build/reproducible-path/gromacs-2020.6/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory 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/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem 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/build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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/build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && 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/build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/parser.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build Scanning dependencies of target release-version-info Scanning dependencies of target thread_mpi /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/scanner.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/mpich-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/mpich-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp Scanning dependencies of target modularsimulator Scanning dependencies of target mdrun_objlib cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build Scanning dependencies of target tng_io_obj make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' [ 1%] Built target thread_mpi cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 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-DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/energyelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' [ 1%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat 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CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2020.6/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include 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-isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 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/build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external 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/build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem 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/build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 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/build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem 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/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem 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-I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong 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-fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich 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-I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/mpich-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/mpich/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/mpich/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 0%] Built target scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 0%] Built target release-version-info [ 0%] Built target lmfit_objlib /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend [ 2%] Built target tng_io_obj make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 3%] Built target thread_mpi cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color= [ 3%] Built target linearalgebra [ 5%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend Scanning dependencies of target gtest make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/src/gtest-all.cc make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 72%] Built target libgromacs cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../../lib/libgtest.a CMakeFiles/gtest.dir/src/gtest-all.cc.o /usr/bin/ranlib ../../../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 72%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= Scanning dependencies of target gmock make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -D_GNU_SOURCE=1 -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmock.a CMakeFiles/gmock.dir/src/gmock-all.cc.o /usr/bin/ranlib ../../../../lib/libgmock.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 73%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/testutils /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/cmdlinetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/conftest.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/filematchers.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem 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'/build/reproducible-path/gromacs-2020.6/build/mpich' [ 76%] Built target testutils /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend Scanning dependencies of target testutils-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' Scanning dependencies of target selection-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/indexutil.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/mpitest.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/poscalc.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/selectioncollection.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' Scanning dependencies of target testutils-test make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/selectionoption.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/interactivetest.cpp /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/mock_helptopic.cpp Scanning dependencies of target applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' Scanning dependencies of target domdec-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfitting.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests/hashedmap.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/calc_verletbuf.cpp Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmebsplinetest.cpp Scanning dependencies of target utility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/alignedallocator.cpp /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fft/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fft/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fft/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constr.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 77%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestdata.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/refdata_tests.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 77%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 77%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests/localatomsetmanager.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/arrayrefwithpadding.cpp Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fft/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/densityfit.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 77%] Built target fft-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdspan-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 [ 78%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpformat.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 78%] Built target domdec-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' Scanning dependencies of target options-test [ 78%] Built target hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/abstractoptionstorage.cpp Scanning dependencies of target pbcutil-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/xvgtest_tests.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 78%] Built target pbcutil-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 79%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 79%] Built target testutils-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/tables/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/tables/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/tables/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestdata.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 80%] Built target selection-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 80%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= Scanning dependencies of target topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/filenameoption.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settle.cpp [ 80%] Built target applied_forces-test cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 80%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/testhardwarecontexts.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 81%] Built target taskassignment-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/tabulatednormaldistribution.cpp Scanning dependencies of target awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 82%] Built target topology-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/tables/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 83%] Built target ewald-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/optional.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/base.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 84%] Built target pull-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 86%] Built target mdlib-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/grid.cpp /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/threefry.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 86%] Built target table-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreeserializer.cpp Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 86%] Built target mdspan-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/mutex.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/path.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcserializer.cpp [ 87%] Built target awh-test cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/textreader.cpp [ 87%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 89%] Built target math-test cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/timeunitmanager.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 89%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/string_view.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/pargs.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 90%] Built target random-test cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 91%] Built target fileio-test cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/mpich/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 92%] Built target options-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 95%] Built target utility-test cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 96%] Built target commandline-test cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 97%] Built target compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [100%] Built target simd-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/mpich/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' (cd build/mpich; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2020.6/build/mpich/lib \ ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i s390x ) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2020.6/build/mpich/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2020.6/build/mpich/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2020.6/build/mpich/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2020.6/build/mpich/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2020.6/build/mpich Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (4 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (6 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (4 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnys 1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms) 1: [----------] 34 tests from ReferenceDataTest (10 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (0 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (4 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (5 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (21 ms total) 1: [ PASSED ] 59 tests. 1/30 Test #1: TestUtilsUnitTests ............... Passed 0.07 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.mpich "-np" "2" "-host" "localhost" "/build/reproducible-path/gromacs-2020.6/build/mpich/bin/testutils-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (5 ms) 2: [----------] 1 test from MpiSelfTest (13 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (13 ms total) 2: [ PASSED ] 1 test. 2/30 Test #2: TestUtilsMpiUnitTests ............ Passed 0.18 sec test 3 Start 3: UtilityUnitTests 3: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/UtilityUnitTests.xml" 3: Test timeout computed to be: 30 3: [==========] Running 347 tests from 56 test cases. 3: [----------] Global test environment set-up. 3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.Move 3: [ OK ] AllocatorTest/0.Move (0 ms) 3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/0 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.Move 3: [ OK ] AllocatorTest/1.Move (0 ms) 3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/1 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.Move 3: [ OK ] AllocatorTest/2.Move (0 ms) 3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/2 (1 ms total) 3: 3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.Move 3: [ OK ] AllocatorTest/3.Move (0 ms) 3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/3 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.Move 3: [ OK ] AllocatorTest/4.Move (0 ms) 3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/4 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.Move 3: [ OK ] AllocatorTest/5.Move (0 ms) 3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/5 (0 ms total) 3: 3: [----------] 1 test from AllocatorUntypedTest 3: [ RUN ] AllocatorUntypedTest.Comparison 3: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 3: [----------] 1 test from AllocatorUntypedTest (0 ms total) 3: 3: [----------] 1 test from EmptyArrayRefTest 3: [ RUN ] EmptyArrayRefTest.IsEmpty 3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyArrayRefTest (0 ms total) 3: 3: [----------] 1 test from EmptyConstArrayRefTest 3: [ RUN ] EmptyConstArrayRefTest.IsEmpty 3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/5 (5 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/10 (1 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/18 (1 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 3: 3: [----------] 2 tests from CStringUtilityTest 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 3: [----------] 2 tests from CStringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from DefaultInitializationAllocator 3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 3: 3: [----------] 4 tests from EnumerationHelpersTest 3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 3: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 3: 3: [----------] 9 tests from FixedCapacityVectorTest 3: [ RUN ] FixedCapacityVectorTest.IsEmpty 3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PushWorks 3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PopWorks 3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ClearWorks 3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.AtThrows 3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 3: [ RUN ] FixedCapacityVectorTest.IteratorWorks 3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 3: 3: [----------] 5 tests from InMemorySerializerTest 3: [ RUN ] InMemorySerializerTest.Roundtrip 3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SizeIsCorrect 3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 3: [----------] 5 tests from InMemorySerializerTest (0 ms total) 3: 3: [----------] 4 tests from KeyValueTreeSerializerTest 3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 3: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 3: 3: [----------] 6 tests from TreeValueTransformTest 3: [ RUN ] TreeValueTransformTest.SimpleTransforms 3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (4 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromString 3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms) 3: [ RUN ] TreeValueTransformTest.ScopedTransformRules 3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 3: [----------] 6 tests from TreeValueTransformTest (5 ms total) 3: 3: [----------] 1 test from TreeValueTransformErrorTest 3: [ RUN ] TreeValueTransformErrorTest.ConversionError 3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 3: 3: [----------] 7 tests from LoggerTest 3: [ RUN ] LoggerTest.EmptyLoggerWorks 3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToStream 3: [ OK ] LoggerTest.LogsToStream (0 ms) 3: [ RUN ] LoggerTest.LogsToFile 3: [ OK ] LoggerTest.LogsToFile (0 ms) 3: [ RUN ] LoggerTest.LevelFilteringWorks 3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleStreams 3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleFiles 3: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 3: [ RUN ] LoggerTest.LogsToStreamAndFile 3: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms) 3: [----------] 7 tests from LoggerTest (1 ms total) 3: 3: [----------] 4 tests from MutexBasicTest 3: [ RUN ] MutexBasicTest.CanBeMade 3: [ OK ] MutexBasicTest.CanBeMade (0 ms) 3: [ RUN ] MutexBasicTest.CanBeLocked 3: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeTryLocked 3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 3: [----------] 4 tests from MutexBasicTest (0 ms total) 3: 3: [----------] 3 tests from MutexTaskTest 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (5 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (4 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 3: [----------] 3 tests from MutexTaskTest (9 ms total) 3: 3: [----------] 2 tests from PathTest 3: [ RUN ] PathTest.StripSourcePrefixWorks 3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 3: [ RUN ] PathTest.SearchOperationsWork 3: [ OK ] PathTest.SearchOperationsWork (1 ms) 3: [----------] 2 tests from PathTest (1 ms total) 3: 3: [----------] 2 tests from PhysicalNodeCommunicatorTest 3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 3: 3: [----------] 9 tests from StringUtilityTest 3: [ RUN ] StringUtilityTest.StartsWith 3: [ OK ] StringUtilityTest.StartsWith (0 ms) 3: [ RUN ] StringUtilityTest.EndsWith 3: [ OK ] StringUtilityTest.EndsWith (0 ms) 3: [ RUN ] StringUtilityTest.StripSuffixIfPresent 3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 3: [ RUN ] StringUtilityTest.StripString 3: [ OK ] StringUtilityTest.StripString (0 ms) 3: [ RUN ] StringUtilityTest.SplitString 3: [ OK ] StringUtilityTest.SplitString (0 ms) 3: [ RUN ] StringUtilityTest.SplitDelimitedString 3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 3: [----------] 9 tests from StringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from FormatStringTest 3: [ RUN ] FormatStringTest.HandlesBasicFormatting 3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 3: [ RUN ] FormatStringTest.HandlesLongStrings 3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 3: [----------] 2 tests from FormatStringTest (0 ms total) 3: 3: [----------] 1 test from StringFormatterTest 3: [ RUN ] StringFormatterTest.HandlesBasicFormatting 3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 3: [----------] 1 test from StringFormatterTest (0 ms total) 3: 3: [----------] 1 test from formatAndJoinTest 3: [ RUN ] formatAndJoinTest.Works 3: [ OK ] formatAndJoinTest.Works (0 ms) 3: [----------] 1 test from formatAndJoinTest (0 ms total) 3: 3: [----------] 1 test from JoinStringsTest 3: [ RUN ] JoinStringsTest.Works 3: [ OK ] JoinStringsTest.Works (0 ms) 3: [----------] 1 test from JoinStringsTest (0 ms total) 3: 3: [----------] 6 tests from ReplaceAllTest 3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesNoMatches 3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 3: [----------] 6 tests from ReplaceAllTest (1 ms total) 3: 3: [----------] 10 tests from TextLineWrapperTest 3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectly 3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndent 3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 3: [----------] 10 tests from TextLineWrapperTest (0 ms total) 3: 3: [----------] 6 tests from TextWriterTest 3: [ RUN ] TextWriterTest.WritesLines 3: [ OK ] TextWriterTest.WritesLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInParts 3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 3: [ RUN ] TextWriterTest.WritesWrappedLines 3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 3: [ RUN ] TextWriterTest.TracksNewlines 3: [ OK ] TextWriterTest.TracksNewlines (1 ms) 3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 3: [----------] 6 tests from TextWriterTest (1 ms total) 3: 3: [----------] 1 test from TypeTraitsTest 3: [ RUN ] TypeTraitsTest.IsIntegralConstant 3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 3: [----------] 1 test from TypeTraitsTest (0 ms total) 3: 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 3: 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (5 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (20 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (20 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (17 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (12 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (15 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (89 ms total) 3: 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 347 tests from 56 test cases ran. (119 ms total) 3: [ PASSED ] 347 tests. 3/30 Test #3: UtilityUnitTests ................. Passed 0.18 sec test 4 Start 4: UtilityMpiUnitTests 4: Test command: /usr/bin/mpiexec.mpich "-np" "4" "-host" "localhost" "/build/reproducible-path/gromacs-2020.6/build/mpich/bin/utility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/UtilityMpiUnitTests.xml" 4: Test timeout computed to be: 30 4: [==========] Running 2 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from PhysicalNodeCommunicatorTest 4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (16 ms) 4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (24 ms) 4: [----------] 2 tests from PhysicalNodeCommunicatorTest (56 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test case ran. (56 ms total) 4: [ PASSED ] 2 tests. 4/30 Test #4: UtilityMpiUnitTests .............. Passed 0.34 sec test 5 Start 5: MdlibUnitTest 5: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/MdlibUnitTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 187 tests from 13 test cases. 5: [----------] Global test environment set-up. 5: [----------] 1 test from VerletBufferConstraintTest 5: [ RUN ] VerletBufferConstraintTest.EqualMasses 5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 5: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 5: 5: [----------] 2 tests from PrEbinTest 5: [ RUN ] PrEbinTest.HandlesAverages 5: [ OK ] PrEbinTest.HandlesAverages (0 ms) 5: [ RUN ] PrEbinTest.HandlesEmptyAverages 5: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 5: [----------] 2 tests from PrEbinTest (1 ms total) 5: 5: [----------] 4 tests from ShakeTest 5: [ RUN ] ShakeTest.ConstrainsOneBond 5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 5: [----------] 4 tests from ShakeTest (0 ms total) 5: 5: [----------] 1 test from NullSignalTest 5: [ RUN ] NullSignalTest.NullSignallerWorks 5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 5: [----------] 1 test from NullSignalTest (0 ms total) 5: 5: [----------] 7 tests from SignalTest 5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 5: [----------] 7 tests from SignalTest (0 ms total) 5: 5: [----------] 9 tests from UpdateGroups 5: [ RUN ] UpdateGroups.ethaneUA 5: [ OK ] UpdateGroups.ethaneUA (0 ms) 5: [ RUN ] UpdateGroups.methane 5: [ OK ] UpdateGroups.methane (0 ms) 5: [ RUN ] UpdateGroups.ethane 5: [ OK ] UpdateGroups.ethane (0 ms) 5: [ RUN ] UpdateGroups.butaneUA 5: [ OK ] UpdateGroups.butaneUA (0 ms) 5: [ RUN ] UpdateGroups.waterThreeSite 5: [ OK ] UpdateGroups.waterThreeSite (0 ms) 5: [ RUN ] UpdateGroups.waterFourSite 5: [ OK ] UpdateGroups.waterFourSite (0 ms) 5: [ RUN ] UpdateGroups.fourAtomsWithSettle 5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 5: [ RUN ] UpdateGroups.waterFlexAngle 5: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 5: [ RUN ] UpdateGroups.twoMoltypes 5: [ OK ] UpdateGroups.twoMoltypes (0 ms) 5: [----------] 9 tests from UpdateGroups (0 ms total) 5: 5: [----------] 1 test from UpdateGroupsCog 5: [ RUN ] UpdateGroupsCog.ComputesCogs 5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 5: [----------] 1 test from UpdateGroupsCog (1 ms total) 5: 5: [----------] 84 tests from WithParameters/ConstraintsTest 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms) 5: [----------] 84 tests from WithParameters/ConstraintsTest (7 ms total) 5: 5: [----------] 11 tests from WithParameters/EnergyOutputTest 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 5: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (13 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (6 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 5: Opened /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (2 ms) 5: [----------] 11 tests from WithParameters/EnergyOutputTest (48 ms total) 5: 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (1 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (1 ms total) 5: 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 5: 5: [----------] 16 tests from WithParameters/LeapFrogTest 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (10 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (5 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (5 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (6 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (9 ms) 5: [----------] 16 tests from WithParameters/LeapFrogTest (45 ms total) 5: 5: [----------] 13 tests from WithParameters/SettleTest 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 5: [----------] 13 tests from WithParameters/SettleTest (7 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 187 tests from 13 test cases ran. (110 ms total) 5: [ PASSED ] 187 tests. 5/30 Test #5: MdlibUnitTest .................... Passed 0.18 sec test 6 Start 6: AppliedForcesUnitTest 6: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/AppliedForcesUnitTest.xml" 6: Test timeout computed to be: 30 6: [==========] Running 20 tests from 4 test cases. 6: [----------] Global test environment set-up. 6: [----------] 2 tests from DensityFittingTest 6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms) 6: [ RUN ] DensityFittingTest.SingleAtom 6: [ OK ] DensityFittingTest.SingleAtom (0 ms) 6: [----------] 2 tests from DensityFittingTest (1 ms total) 6: 6: [----------] 8 tests from DensityFittingOptionsTest 6: [ RUN ] DensityFittingOptionsTest.DefaultParameters 6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 6: [ RUN ] DensityFittingOptionsTest.KvtToInternal 6: [ OK ] DensityFittingOptionsTest.KvtToInternal (1 ms) 6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 6: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 6: 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest 6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 6: 6: [----------] 3 tests from ElectricFieldTest 6: [ RUN ] ElectricFieldTest.Static 6: [ OK ] ElectricFieldTest.Static (0 ms) 6: [ RUN ] ElectricFieldTest.Oscillating 6: [ OK ] ElectricFieldTest.Oscillating (0 ms) 6: [ RUN ] ElectricFieldTest.Pulsed 6: [ OK ] ElectricFieldTest.Pulsed (0 ms) 6: [----------] 3 tests from ElectricFieldTest (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 20 tests from 4 test cases ran. (2 ms total) 6: [ PASSED ] 20 tests. 6/30 Test #6: AppliedForcesUnitTest ............ Passed 0.05 sec test 7 Start 7: CommandLineUnitTests 7: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/CommandLineUnitTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 59 tests from 7 test cases. 7: [----------] Global test environment set-up. 7: [----------] 3 tests from CommandLineHelpModuleTest 7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 7: [----------] 3 tests from CommandLineHelpModuleTest (6 ms total) 7: 7: [----------] 7 tests from CommandLineHelpWriterTest 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 7: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 7: 7: [----------] 6 tests from CommandLineModuleManagerTest 7: [ RUN ] CommandLineModuleManagerTest.RunsModule 7: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 7: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 7: 7: [----------] 13 tests from CommandLineParserTest 7: [ RUN ] CommandLineParserTest.HandlesSingleValues 7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms) 7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesString 7: [ OK ] CommandLineParserTest.HandlesString (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 7: [----------] 13 tests from CommandLineParserTest (1 ms total) 7: 7: [----------] 6 tests from CommandLineProgramContextTest 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 7: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 7: 7: [----------] 3 tests from OutputNamesTest 7: [ RUN ] OutputNamesTest.CanBeSuffixed 7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 7: [----------] 3 tests from OutputNamesTest (0 ms total) 7: 7: [----------] 21 tests from ParseCommonArgsTest 7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (1 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 7: [----------] 21 tests from ParseCommonArgsTest (2 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 59 tests from 7 test cases ran. (10 ms total) 7: [ PASSED ] 59 tests. 7/30 Test #7: CommandLineUnitTests ............. Passed 0.07 sec test 8 Start 8: DomDecTests 8: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/DomDecTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 9 tests from 2 test cases. 8: [----------] Global test environment set-up. 8: [----------] 7 tests from HashedMap 8: [ RUN ] HashedMap.InsertsFinds 8: [ OK ] HashedMap.InsertsFinds (0 ms) 8: [ RUN ] HashedMap.NegativeKeysWork 8: [ OK ] HashedMap.NegativeKeysWork (0 ms) 8: [ RUN ] HashedMap.InsertsErases 8: [ OK ] HashedMap.InsertsErases (0 ms) 8: [ RUN ] HashedMap.InsertsOrAssigns 8: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 8: [ RUN ] HashedMap.Clears 8: [ OK ] HashedMap.Clears (0 ms) 8: [ RUN ] HashedMap.LinkedEntries 8: [ OK ] HashedMap.LinkedEntries (0 ms) 8: [ RUN ] HashedMap.ResizesTable 8: [ OK ] HashedMap.ResizesTable (0 ms) 8: [----------] 7 tests from HashedMap (0 ms total) 8: 8: [----------] 2 tests from LocalAtomSetManager 8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 8: [----------] 2 tests from LocalAtomSetManager (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 9 tests from 2 test cases ran. (0 ms total) 8: [ PASSED ] 9 tests. 8/30 Test #8: DomDecTests ...................... Passed 0.05 sec test 9 Start 9: EwaldUnitTests 9: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/EwaldUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 257 tests from 10 test cases. 9: [----------] Global test environment set-up. 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (11 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (12 ms total) 9: 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (14 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (14 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (15 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (14 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (9 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (9 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (128 ms total) 9: 9: [----------] 144 tests from SaneInput/PmeGatherTest 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (13 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (12 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (13 ms) 9: [----------] 144 tests from SaneInput/PmeGatherTest (128 ms total) 9: 9: [----------] 16 tests from SaneInput/PmeSolveTest 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (9 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (9 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (13 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (1 ms) 9: [----------] 16 tests from SaneInput/PmeSolveTest (47 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (9 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (9 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (23 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (9 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (0 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (10 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (25 ms total) 9: 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (14 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (10 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (9 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (1 ms) 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (46 ms total) 9: 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (15 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (10 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (9 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (1 ms) 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (54 ms total) 9: 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (13 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (3 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (52 ms total) 9: 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (12 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (14 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (14 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (12 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (13 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (13 ms) 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (100 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 257 tests from 10 test cases ran. (790 ms total) 9: [ PASSED ] 257 tests. 9/30 Test #9: EwaldUnitTests ................... Passed 0.89 sec test 10 Start 10: FFTUnitTests 10: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/FFTUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 14 tests from 4 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from ManyFFTTest 10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (17 ms) 10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (57 ms) 10: [----------] 2 tests from ManyFFTTest (75 ms total) 10: 10: [----------] 1 test from FFTTest 10: [ RUN ] FFTTest.Real2DLength18_15Test 10: [ OK ] FFTTest.Real2DLength18_15Test (16 ms) 10: [----------] 1 test from FFTTest (16 ms total) 10: 10: [----------] 1 test from FFFTest3D 10: [ RUN ] FFFTest3D.Real5_6_9 10: [ OK ] FFFTest3D.Real5_6_9 (7 ms) 10: [----------] 1 test from FFFTest3D (7 ms total) 10: 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (6 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (9 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (10 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (35 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (48 ms) 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (112 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 14 tests from 4 test cases ran. (215 ms total) 10: [ PASSED ] 14 tests. 10/30 Test #10: FFTUnitTests ..................... Passed 0.26 sec test 11 Start 11: GpuUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/GpuUtilsUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 62 tests from 20 test cases. 11: [----------] Global test environment set-up. 11: [----------] 2 tests from ClfftInitializer 11: [ RUN ] ClfftInitializer.SingleInitializationWorks 11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 11: [ RUN ] ClfftInitializer.TwoInitializationsWork 11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 11: [----------] 2 tests from ClfftInitializer (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Swap 11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Comparison 11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Swap 11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Comparison 11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/1 (7 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Swap 11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Comparison 11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Swap 11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Comparison 11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 11: 11: [----------] 1 test from HostAllocatorUntypedTest 11: [ RUN ] HostAllocatorUntypedTest.Comparison 11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/3 (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 62 tests from 20 test cases ran. (7 ms total) 11: [ PASSED ] 62 tests. 11/30 Test #11: GpuUtilsUnitTests ................ Passed 0.06 sec test 12 Start 12: HardwareUnitTests 12: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/HardwareUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 4 tests from 1 test case. 12: [----------] Global test environment set-up. 12: [----------] 4 tests from HardwareTopologyTest 12: [ RUN ] HardwareTopologyTest.Execute 12: [ OK ] HardwareTopologyTest.Execute (97 ms) 12: [ RUN ] HardwareTopologyTest.HwlocExecute 12: [ OK ] HardwareTopologyTest.HwlocExecute (101 ms) 12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (93 ms) 12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (115 ms) 12: [----------] 4 tests from HardwareTopologyTest (406 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 4 tests from 1 test case ran. (407 ms total) 12: [ PASSED ] 4 tests. 12/30 Test #12: HardwareUnitTests ................ Passed 0.45 sec test 13 Start 13: MathUnitTests 13: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/MathUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 204 tests from 29 test cases. 13: [----------] Global test environment set-up. 13: [----------] 1 test from EmptyArrayRefWithPaddingTest 13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 13: 13: [----------] 8 tests from TranslateAndScaleTest 13: [ RUN ] TranslateAndScaleTest.identityTransformation 13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingIdentity 13: [ OK ] TranslateAndScaleTest.scalingIdentity (1 ms) 13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 13: [----------] 8 tests from TranslateAndScaleTest (1 ms total) 13: 13: [----------] 12 tests from DensitySimilarityTest 13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (62 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (63 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (56 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 13: [----------] 12 tests from DensitySimilarityTest (181 ms total) 13: 13: [----------] 6 tests from StructureSimilarityTest 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 13: [----------] 6 tests from StructureSimilarityTest (0 ms total) 13: 13: [----------] 8 tests from ExponentialMovingAverage 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 13: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 13: 13: [----------] 21 tests from FunctionTest 13: [ RUN ] FunctionTest.StaticLog2 13: [ OK ] FunctionTest.StaticLog2 (8 ms) 13: [ RUN ] FunctionTest.Log2I32Bit 13: [ OK ] FunctionTest.Log2I32Bit (0 ms) 13: [ RUN ] FunctionTest.Log2I64Bit 13: [ OK ] FunctionTest.Log2I64Bit (0 ms) 13: [ RUN ] FunctionTest.GreatestCommonDivisor 13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 13: [ RUN ] FunctionTest.InvsqrtFloat 13: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvsqrtDouble 13: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvsqrtInteger 13: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 13: [ RUN ] FunctionTest.InvcbrtFloat 13: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvcbrtDouble 13: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvcbrtInteger 13: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 13: [ RUN ] FunctionTest.SixthrootFloat 13: [ OK ] FunctionTest.SixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.SixthrootDouble 13: [ OK ] FunctionTest.SixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.SixthrootInteger 13: [ OK ] FunctionTest.SixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootFloat 13: [ OK ] FunctionTest.InvsixthrootFloat (1 ms) 13: [ RUN ] FunctionTest.InvsixthrootDouble 13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootInteger 13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.Powers 13: [ OK ] FunctionTest.Powers (0 ms) 13: [ RUN ] FunctionTest.ErfInvFloat 13: [ OK ] FunctionTest.ErfInvFloat (0 ms) 13: [ RUN ] FunctionTest.ErfInvDouble 13: [ OK ] FunctionTest.ErfInvDouble (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 13: [----------] 21 tests from FunctionTest (10 ms total) 13: 13: [----------] 4 tests from GaussianOn1DLattice 13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 13: [ RUN ] GaussianOn1DLattice.isCorrect 13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 13: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 13: 13: [----------] 9 tests from GaussTransformTest 13: [ RUN ] GaussTransformTest.isZeroUponConstruction 13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 13: [ RUN ] GaussTransformTest.view 13: [ OK ] GaussTransformTest.view (0 ms) 13: [----------] 9 tests from GaussTransformTest (1 ms total) 13: 13: [----------] 3 tests from DensityFittingForce 13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 13: [ RUN ] DensityFittingForce.pullsTowardsDerivative 13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 13: [----------] 3 tests from DensityFittingForce (0 ms total) 13: 13: [----------] 2 tests from InvertMatrixTest 13: [ RUN ] InvertMatrixTest.IdentityIsImpotent 13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertMatrixTest.ComputesInverse 13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 13: [----------] 2 tests from InvertMatrixTest (0 ms total) 13: 13: [----------] 2 tests from InvertBoxMatrixTest 13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 13: 13: [----------] 15 tests from MatrixTest 13: [ RUN ] MatrixTest.canSetFromArray 13: [ OK ] MatrixTest.canSetFromArray (0 ms) 13: [ RUN ] MatrixTest.canSetStaticallyFromList 13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 13: [ RUN ] MatrixTest.canConstructAndFill 13: [ OK ] MatrixTest.canConstructAndFill (0 ms) 13: [ RUN ] MatrixTest.canSetValues 13: [ OK ] MatrixTest.canSetValues (0 ms) 13: [ RUN ] MatrixTest.canCopyAssign 13: [ OK ] MatrixTest.canCopyAssign (0 ms) 13: [ RUN ] MatrixTest.canSwap 13: [ OK ] MatrixTest.canSwap (0 ms) 13: [ RUN ] MatrixTest.staticMultiDimArrayExtent 13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MatrixTest.determinantWorks 13: [ OK ] MatrixTest.determinantWorks (0 ms) 13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 13: [ RUN ] MatrixTest.traceWorks 13: [ OK ] MatrixTest.traceWorks (0 ms) 13: [ RUN ] MatrixTest.transposeWorks 13: [ OK ] MatrixTest.transposeWorks (0 ms) 13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 13: [ RUN ] MatrixTest.canFillLegacyMatrix 13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 13: [----------] 15 tests from MatrixTest (0 ms total) 13: 13: [----------] 25 tests from MultiDimArrayTest 13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapStatic 13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapDynamic 13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToView 13: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToConstView 13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 13: [ RUN ] MultiDimArrayTest.viewBegin 13: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.viewEnd 13: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstBegin 13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstEnd 13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 13: [----------] 25 tests from MultiDimArrayTest (0 ms total) 13: 13: [----------] 4 tests from MultiDimArrayToMdSpanTest 13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanCopyAssign 13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanMoveAssign 13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanSwap 13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanCopyAssign 13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanMoveAssign 13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanSwap 13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanCopyAssign 13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanMoveAssign 13: [ OK ] PaddedVectorTest/2.CanMoveAssign (1 ms) 13: [ RUN ] PaddedVectorTest/2.CanSwap 13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/2 (1 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanCopyAssign 13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanMoveAssign 13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanSwap 13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanCopyAssign 13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanMoveAssign 13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanSwap 13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanCopyAssign 13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanMoveAssign 13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanSwap 13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanCopyAssign 13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanMoveAssign 13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanSwap 13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanCopyAssign 13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanMoveAssign 13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanSwap 13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanCopyAssign 13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanMoveAssign 13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanSwap 13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanCopyAssign 13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanMoveAssign 13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanSwap 13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 13: 13: [----------] 37 tests from RVecTest 13: [ RUN ] RVecTest.CanBeStoredInVector 13: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAsMutable_rvec 13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Array 13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 13: [ RUN ] RVecTest.CanAddRVecToRvec 13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanAddAssignRVecToRvec 13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractRVecFromRvec 13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanDotProductRVecByRvec 13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanCrossProductRVecByRvec 13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVecInplace 13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 13: [ RUN ] RVecTest.CanScaleRVec 13: [ OK ] RVecTest.CanScaleRVec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVec 13: [ OK ] RVecTest.CanDivideRVec (0 ms) 13: [ RUN ] RVecTest.CanDoUnitvFromRVec 13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanSqLengthOfRVec 13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanLengthOfRVec 13: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToRVec 13: [ OK ] RVecTest.CanCastToRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToDVec 13: [ OK ] RVecTest.CanCastToDVec (0 ms) 13: [ RUN ] RVecTest.CanLeftScalarMultiply 13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanRightScalarMultiply 13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanGetUnitvFromRVec 13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanGetSqLengthOfRVec 13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanGetLengthOfRVec 13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoCrossProductOfRVec 13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoDotProductOfRVec 13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanScaleByVector 13: [ OK ] RVecTest.CanScaleByVector (0 ms) 13: [ RUN ] RVecTest.asIVec 13: [ OK ] RVecTest.asIVec (0 ms) 13: [ RUN ] RVecTest.elementWiseMin 13: [ OK ] RVecTest.elementWiseMin (0 ms) 13: [ RUN ] RVecTest.elementWiseMax 13: [ OK ] RVecTest.elementWiseMax (0 ms) 13: [ RUN ] RVecTest.WorksAs_dvec_Reference 13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_ivec_Reference 13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Reference 13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 13: [ RUN ] RVecTest.CopyConstructorWorks 13: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 13: [ RUN ] RVecTest.CopyAssignmentWorks 13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] RVecTest.MoveConstructorWorks 13: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 13: [ RUN ] RVecTest.MoveAssignmentWorks 13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 13: [----------] 37 tests from RVecTest (2 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 204 tests from 29 test cases ran. (196 ms total) 13: [ PASSED ] 204 tests. 13/30 Test #13: MathUnitTests .................... Passed 0.26 sec test 14 Start 14: MdrunUtilityUnitTests 14: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/MdrunUtilityUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 17 tests from 1 test case. 14: [----------] Global test environment set-up. 14: [----------] 17 tests from ThreadAffinityTest 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 14: NOTE: Affinity setting failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (14 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 14: NOTE: Affinity setting for 1/2 threads failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 14: [----------] 17 tests from ThreadAffinityTest (17 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 17 tests from 1 test case ran. (25 ms total) 14: [ PASSED ] 17 tests. 14/30 Test #14: MdrunUtilityUnitTests ............ Passed 0.08 sec test 15 Start 15: MdrunUtilityMpiUnitTests 15: Test command: /usr/bin/mpiexec.mpich "-np" "4" "-host" "localhost" "/build/reproducible-path/gromacs-2020.6/build/mpich/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 13 tests from 2 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from ThreadAffinityMultiRankTest 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (80 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (37 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (41 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (56 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (44 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (40 ms) 15: [----------] 6 tests from ThreadAffinityMultiRankTest (371 ms total) 15: 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (41 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (56 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (41 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (41 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (56 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (33 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (57 ms) 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (424 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 13 tests from 2 test cases ran. (796 ms total) 15: [ PASSED ] 13 tests. 15/30 Test #15: MdrunUtilityMpiUnitTests ......... Passed 1.12 sec test 16 Start 16: MDSpanTests 16: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/MDSpanTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 32 tests from 7 test cases. 16: [----------] Global test environment set-up. 16: [----------] 4 tests from BasicAccessorPolicy 16: [ RUN ] BasicAccessorPolicy.Decay 16: [ OK ] BasicAccessorPolicy.Decay (0 ms) 16: [ RUN ] BasicAccessorPolicy.Access 16: [ OK ] BasicAccessorPolicy.Access (1 ms) 16: [ RUN ] BasicAccessorPolicy.Offset 16: [ OK ] BasicAccessorPolicy.Offset (0 ms) 16: [ RUN ] BasicAccessorPolicy.CopyAccessor 16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 16: [----------] 4 tests from BasicAccessorPolicy (1 ms total) 16: 16: [----------] 4 tests from ExtentsTest 16: [ RUN ] ExtentsTest.Construction 16: [ OK ] ExtentsTest.Construction (0 ms) 16: [ RUN ] ExtentsTest.PurelyStatic 16: [ OK ] ExtentsTest.PurelyStatic (0 ms) 16: [ RUN ] ExtentsTest.RankNought 16: [ OK ] ExtentsTest.RankNought (0 ms) 16: [ RUN ] ExtentsTest.Assignment 16: [ OK ] ExtentsTest.Assignment (0 ms) 16: [----------] 4 tests from ExtentsTest (0 ms total) 16: 16: [----------] 8 tests from MdSpanExtension 16: [ RUN ] MdSpanExtension.SlicingAllStatic 16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingDynamic 16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingAllStatic3D 16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 16: [ RUN ] MdSpanExtension.SlicingEqualsView3D 16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 16: [ RUN ] MdSpanExtension.additionWorks 16: [ OK ] MdSpanExtension.additionWorks (0 ms) 16: [ RUN ] MdSpanExtension.subtractionWorks 16: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 16: [ RUN ] MdSpanExtension.multiplicationWorks 16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 16: [ RUN ] MdSpanExtension.divisionWorks 16: [ OK ] MdSpanExtension.divisionWorks (0 ms) 16: [----------] 8 tests from MdSpanExtension (0 ms total) 16: 16: [----------] 3 tests from LayoutTests 16: [ RUN ] LayoutTests.LayoutRightConstruction 16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 16: [ RUN ] LayoutTests.LayoutRightProperties 16: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 16: [ RUN ] LayoutTests.LayoutRightOperator 16: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 16: [----------] 3 tests from LayoutTests (0 ms total) 16: 16: [----------] 1 test from MdSpanTest 16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 16: [----------] 1 test from MdSpanTest (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/0.Rank 16: [ OK ] MdSpanTest/0.Rank (0 ms) 16: [ RUN ] MdSpanTest/0.DynamicRank 16: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/0.Extents 16: [ OK ] MdSpanTest/0.Extents (0 ms) 16: [ RUN ] MdSpanTest/0.Strides 16: [ OK ] MdSpanTest/0.Strides (0 ms) 16: [ RUN ] MdSpanTest/0.Properties 16: [ OK ] MdSpanTest/0.Properties (0 ms) 16: [ RUN ] MdSpanTest/0.Operator 16: [ OK ] MdSpanTest/0.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/0 (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/1.Rank 16: [ OK ] MdSpanTest/1.Rank (0 ms) 16: [ RUN ] MdSpanTest/1.DynamicRank 16: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/1.Extents 16: [ OK ] MdSpanTest/1.Extents (0 ms) 16: [ RUN ] MdSpanTest/1.Strides 16: [ OK ] MdSpanTest/1.Strides (0 ms) 16: [ RUN ] MdSpanTest/1.Properties 16: [ OK ] MdSpanTest/1.Properties (0 ms) 16: [ RUN ] MdSpanTest/1.Operator 16: [ OK ] MdSpanTest/1.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/1 (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 32 tests from 7 test cases ran. (1 ms total) 16: [ PASSED ] 32 tests. 16/30 Test #16: MDSpanTests ...................... Passed 0.05 sec test 17 Start 17: OnlineHelpUnitTests 17: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/OnlineHelpUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 22 tests from 4 test cases. 17: [----------] Global test environment set-up. 17: [----------] 6 tests from TextTableFormatterTest 17: [ RUN ] TextTableFormatterTest.HandlesBasicCase 17: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesIndentation 17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 17: [----------] 6 tests from TextTableFormatterTest (1 ms total) 17: 17: [----------] 3 tests from HelpManagerTest 17: [ RUN ] HelpManagerTest.HandlesRootTopic 17: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 17: [ RUN ] HelpManagerTest.HandlesSubTopics 17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 17: [ RUN ] HelpManagerTest.HandlesInvalidTopics 17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 17: [----------] 3 tests from HelpManagerTest (0 ms total) 17: 17: [----------] 2 tests from HelpTopicFormattingTest 17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 17: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 17: 17: [----------] 11 tests from HelpWriterContextTest 17: [ RUN ] HelpWriterContextTest.FormatsParagraphs 17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralText 17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsBulletList 17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsGridTable 17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsTitles 17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 17: [----------] 11 tests from HelpWriterContextTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 22 tests from 4 test cases ran. (2 ms total) 17: [ PASSED ] 22 tests. 17/30 Test #17: OnlineHelpUnitTests .............. Passed 0.05 sec test 18 Start 18: OptionsUnitTests 18: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/OptionsUnitTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 110 tests from 18 test cases. 18: [----------] Global test environment set-up. 18: [----------] 5 tests from AbstractOptionStorageTest 18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 18: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 18: 18: [----------] 8 tests from FileNameOptionTest 18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 18: [----------] 8 tests from FileNameOptionTest (0 ms total) 18: 18: [----------] 15 tests from FileNameOptionManagerTest 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 18: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 18: 18: [----------] 1 test from OptionsTest 18: [ RUN ] OptionsTest.FailsOnNonsafeStorage 18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 18: [----------] 1 test from OptionsTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerTest 18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMissingValue 18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesExtraValue 18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesGroups 18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesSections 18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 18: [----------] 9 tests from OptionsAssignerTest (0 ms total) 18: 18: [----------] 4 tests from OptionsAssignerBooleanTest 18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 18: 18: [----------] 13 tests from OptionsAssignerIntegerTest 18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 18: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 18: 18: [----------] 5 tests from OptionsAssignerDoubleTest 18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerStringTest 18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 9 tests from OptionsAssignerStringTest (1 ms total) 18: 18: [----------] 6 tests from OptionsAssignerEnumTest 18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 18: 18: [----------] 8 tests from RepeatingOptionSectionTest 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 18: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 18: 18: [----------] 1 test from TimeUnitManagerTest 18: [ RUN ] TimeUnitManagerTest.BasicOperations 18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 18: [----------] 1 test from TimeUnitManagerTest (0 ms total) 18: 18: [----------] 4 tests from TimeUnitBehaviorTest 18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 18: 18: [----------] 2 tests from TreeValueSupportAssignTest 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 18: 18: [----------] 1 test from TreeValueSupportAssignErrorTest 18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 18: 18: [----------] 5 tests from TreeValueSupportCheckTest 18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 18: 18: [----------] 6 tests from TreeValueSupportAdjustTest 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 18: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 18: 18: [----------] 8 tests from TreeValueSupportTest 18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsInt64Option 18: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsStringOption 18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsFloatOption 18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumOption 18: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms) 18: [----------] 8 tests from TreeValueSupportTest (1 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 110 tests from 18 test cases ran. (5 ms total) 18: [ PASSED ] 110 tests. 18/30 Test #18: OptionsUnitTests ................. Passed 0.07 sec test 19 Start 19: PbcutilUnitTest 19: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/PbcutilUnitTest.xml" 19: Test timeout computed to be: 30 19: [==========] Running 3 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 1 test from PbcTest 19: [ RUN ] PbcTest.CalcShiftsWorks 19: [ OK ] PbcTest.CalcShiftsWorks (1 ms) 19: [----------] 1 test from PbcTest (1 ms total) 19: 19: [----------] 2 tests from PbcEnumsTest 19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 19: [----------] 2 tests from PbcEnumsTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 3 tests from 2 test cases ran. (1 ms total) 19: [ PASSED ] 3 tests. 19/30 Test #19: PbcutilUnitTest .................. Passed 0.05 sec test 20 Start 20: RandomUnitTests 20: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/RandomUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 44 tests from 10 test cases. 20: [----------] Global test environment set-up. 20: [----------] 4 tests from ExponentialDistributionTest 20: [ RUN ] ExponentialDistributionTest.Output 20: [ OK ] ExponentialDistributionTest.Output (0 ms) 20: [ RUN ] ExponentialDistributionTest.Logical 20: [ OK ] ExponentialDistributionTest.Logical (0 ms) 20: [ RUN ] ExponentialDistributionTest.Reset 20: [ OK ] ExponentialDistributionTest.Reset (0 ms) 20: [ RUN ] ExponentialDistributionTest.AltParam 20: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 20: 20: [----------] 4 tests from GammaDistributionTest 20: [ RUN ] GammaDistributionTest.Output 20: [ OK ] GammaDistributionTest.Output (1 ms) 20: [ RUN ] GammaDistributionTest.Logical 20: [ OK ] GammaDistributionTest.Logical (0 ms) 20: [ RUN ] GammaDistributionTest.Reset 20: [ OK ] GammaDistributionTest.Reset (0 ms) 20: [ RUN ] GammaDistributionTest.AltParam 20: [ OK ] GammaDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from GammaDistributionTest (1 ms total) 20: 20: [----------] 4 tests from NormalDistributionTest 20: [ RUN ] NormalDistributionTest.Output 20: [ OK ] NormalDistributionTest.Output (0 ms) 20: [ RUN ] NormalDistributionTest.Logical 20: [ OK ] NormalDistributionTest.Logical (0 ms) 20: [ RUN ] NormalDistributionTest.Reset 20: [ OK ] NormalDistributionTest.Reset (0 ms) 20: [ RUN ] NormalDistributionTest.AltParam 20: [ OK ] NormalDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from NormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from SeedTest 20: [ RUN ] SeedTest.makeRandomSeed 20: [ OK ] SeedTest.makeRandomSeed (0 ms) 20: [----------] 1 test from SeedTest (0 ms total) 20: 20: [----------] 6 tests from TabulatedNormalDistributionTest 20: [ RUN ] TabulatedNormalDistributionTest.Output14 20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Output16 20: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Logical 20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Reset 20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.AltParam 20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 20: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from TabulatedNormalDistributionTableTest 20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (5 ms) 20: [----------] 1 test from TabulatedNormalDistributionTableTest (5 ms total) 20: 20: [----------] 6 tests from ThreeFry2x64Test 20: [ RUN ] ThreeFry2x64Test.Logical 20: [ OK ] ThreeFry2x64Test.Logical (0 ms) 20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 20: [ RUN ] ThreeFry2x64Test.Reseed 20: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 20: [ RUN ] ThreeFry2x64Test.Discard 20: [ OK ] ThreeFry2x64Test.Discard (0 ms) 20: [ RUN ] ThreeFry2x64Test.InvalidCounter 20: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms) 20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 20: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 20: 20: [----------] 4 tests from UniformIntDistributionTest 20: [ RUN ] UniformIntDistributionTest.Output 20: [ OK ] UniformIntDistributionTest.Output (0 ms) 20: [ RUN ] UniformIntDistributionTest.Logical 20: [ OK ] UniformIntDistributionTest.Logical (0 ms) 20: [ RUN ] UniformIntDistributionTest.Reset 20: [ OK ] UniformIntDistributionTest.Reset (0 ms) 20: [ RUN ] UniformIntDistributionTest.AltParam 20: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 20: 20: [----------] 5 tests from UniformRealDistributionTest 20: [ RUN ] UniformRealDistributionTest.GenerateCanonical 20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Output 20: [ OK ] UniformRealDistributionTest.Output (0 ms) 20: [ RUN ] UniformRealDistributionTest.Logical 20: [ OK ] UniformRealDistributionTest.Logical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Reset 20: [ OK ] UniformRealDistributionTest.Reset (0 ms) 20: [ RUN ] UniformRealDistributionTest.AltParam 20: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 20: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 20: 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (1 ms) 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 44 tests from 10 test cases ran. (8 ms total) 20: [ PASSED ] 44 tests. 20/30 Test #20: RandomUnitTests .................. Passed 0.07 sec test 21 Start 21: RestraintTests 21: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/RestraintTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 1 test from 1 test case. 21: [----------] Global test environment set-up. 21: [----------] 1 test from RestraintManager 21: [ RUN ] RestraintManager.restraintList 21: [ OK ] RestraintManager.restraintList (0 ms) 21: [----------] 1 test from RestraintManager (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1 test from 1 test case ran. (0 ms total) 21: [ PASSED ] 1 test. 21/30 Test #21: RestraintTests ................... Passed 0.04 sec test 22 Start 22: TableUnitTests 22: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/TableUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 20 tests from 2 test cases. 22: [----------] Global test environment set-up. 22: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms) 22: [ RUN ] SplineTableTest/0.Sinc 22: [ OK ] SplineTableTest/0.Sinc (0 ms) 22: [ RUN ] SplineTableTest/0.LJ12 22: [ OK ] SplineTableTest/0.LJ12 (31 ms) 22: [ RUN ] SplineTableTest/0.PmeCorrection 22: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/0.TwoFunctions 22: [ OK ] SplineTableTest/0.TwoFunctions (49 ms) 22: [ RUN ] SplineTableTest/0.ThreeFunctions 22: [ OK ] SplineTableTest/0.ThreeFunctions (52 ms) 22: [ RUN ] SplineTableTest/0.Simd 22: [ OK ] SplineTableTest/0.Simd (10 ms) 22: [ RUN ] SplineTableTest/0.SimdTwoFunctions 22: [ OK ] SplineTableTest/0.SimdTwoFunctions (51 ms) 22: [----------] 10 tests from SplineTableTest/0 (201 ms total) 22: 22: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 22: [ RUN ] SplineTableTest/1.Sinc 22: [ OK ] SplineTableTest/1.Sinc (1 ms) 22: [ RUN ] SplineTableTest/1.LJ12 22: [ OK ] SplineTableTest/1.LJ12 (6 ms) 22: [ RUN ] SplineTableTest/1.PmeCorrection 22: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/1.TwoFunctions 22: [ OK ] SplineTableTest/1.TwoFunctions (9 ms) 22: [ RUN ] SplineTableTest/1.ThreeFunctions 22: [ OK ] SplineTableTest/1.ThreeFunctions (8 ms) 22: [ RUN ] SplineTableTest/1.Simd 22: [ OK ] SplineTableTest/1.Simd (1 ms) 22: [ RUN ] SplineTableTest/1.SimdTwoFunctions 22: [ OK ] SplineTableTest/1.SimdTwoFunctions (8 ms) 22: [----------] 10 tests from SplineTableTest/1 (37 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 20 tests from 2 test cases ran. (242 ms total) 22: [ PASSED ] 20 tests. 22/30 Test #22: TableUnitTests ................... Passed 0.30 sec test 23 Start 23: TaskAssignmentUnitTests 23: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/TaskAssignmentUnitTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 2 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms) 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 2 test cases ran. (1 ms total) 23: [ PASSED ] 3 tests. 23/30 Test #23: TaskAssignmentUnitTests .......... Passed 0.05 sec test 24 Start 24: TopologyTest 24: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/TopologyTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 11 tests from 3 test cases. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ExclusionBlockTest 24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 24: [ RUN ] ExclusionBlockTest.MergeExclusions 24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 24: [----------] 3 tests from ExclusionBlockTest (1 ms total) 24: 24: [----------] 2 tests from MtopTest 24: [ RUN ] MtopTest.RangeBasedLoop 24: [ OK ] MtopTest.RangeBasedLoop (0 ms) 24: [ RUN ] MtopTest.Operators 24: [ OK ] MtopTest.Operators (0 ms) 24: [----------] 2 tests from MtopTest (0 ms total) 24: 24: [----------] 6 tests from SymtabTest 24: [ RUN ] SymtabTest.EmptyOnOpen 24: [ OK ] SymtabTest.EmptyOnOpen (0 ms) 24: [ RUN ] SymtabTest.AddSingleEntry 24: [ OK ] SymtabTest.AddSingleEntry (0 ms) 24: [ RUN ] SymtabTest.AddTwoDistinctEntries 24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms) 24: [ RUN ] SymtabTest.TryToAddDuplicates 24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms) 24: [ RUN ] SymtabTest.AddLargeNumberOfEntries 24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms) 24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable 24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms) 24: [----------] 6 tests from SymtabTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 11 tests from 3 test cases ran. (1 ms total) 24: [ PASSED ] 11 tests. 24/30 Test #24: TopologyTest ..................... Passed 0.06 sec test 25 Start 25: PullTest 25: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/PullTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 5 tests from 1 test case. 25: [----------] Global test environment set-up. 25: [----------] 5 tests from PullTest 25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 25: [----------] 5 tests from PullTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 5 tests from 1 test case ran. (6 ms total) 25: [ PASSED ] 5 tests. 25/30 Test #25: PullTest ......................... Passed 0.05 sec test 26 Start 26: AwhTest 26: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/AwhTest.xml" 26: Test timeout computed to be: 30 26: [==========] Running 12 tests from 4 test cases. 26: [----------] Global test environment set-up. 26: [----------] 1 test from BiasTest 26: [ RUN ] BiasTest.DetectsCovering 26: [ OK ] BiasTest.DetectsCovering (1 ms) 26: [----------] 1 test from BiasTest (1 ms total) 26: 26: [----------] 1 test from gridTest 26: [ RUN ] gridTest.neighborhood 26: [ OK ] gridTest.neighborhood (1 ms) 26: [----------] 1 test from gridTest (1 ms total) 26: 26: [----------] 8 tests from WithParameters/BiasTest 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (4 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) 26: [----------] 8 tests from WithParameters/BiasTest (7 ms total) 26: 26: [----------] 2 tests from WithParameters/BiasStateTest 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 26: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 12 tests from 4 test cases ran. (9 ms total) 26: [ PASSED ] 12 tests. 26/30 Test #26: AwhTest .......................... Passed 0.07 sec test 27 Start 27: SimdUnitTests 27: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/SimdUnitTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 288 tests from 22 test cases. 27: [----------] Global test environment set-up. 27: [----------] 9 tests from SimdBootstrapTest 27: [ RUN ] SimdBootstrapTest.loadStore 27: [ OK ] SimdBootstrapTest.loadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.loadU 27: [ OK ] SimdBootstrapTest.loadU (0 ms) 27: [ RUN ] SimdBootstrapTest.storeU 27: [ OK ] SimdBootstrapTest.storeU (0 ms) 27: [ RUN ] SimdBootstrapTest.loadStoreI 27: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 27: [ RUN ] SimdBootstrapTest.loadUI 27: [ OK ] SimdBootstrapTest.loadUI (0 ms) 27: [ RUN ] SimdBootstrapTest.storeUI 27: [ OK ] SimdBootstrapTest.storeUI (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadStore 27: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadU 27: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4StoreU 27: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 27: [----------] 9 tests from SimdBootstrapTest (0 ms total) 27: 27: [----------] 1 test from SimdTest 27: [ RUN ] SimdTest.GmxAligned 27: [ OK ] SimdTest.GmxAligned (0 ms) 27: [----------] 1 test from SimdTest (0 ms total) 27: 27: [----------] 42 tests from SimdFloatingpointTest 27: [ RUN ] SimdFloatingpointTest.setZero 27: [ OK ] SimdFloatingpointTest.setZero (0 ms) 27: [ RUN ] SimdFloatingpointTest.set 27: [ OK ] SimdFloatingpointTest.set (0 ms) 27: [ RUN ] SimdFloatingpointTest.add 27: [ OK ] SimdFloatingpointTest.add (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskAdd 27: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 27: [ RUN ] SimdFloatingpointTest.sub 27: [ OK ] SimdFloatingpointTest.sub (0 ms) 27: [ RUN ] SimdFloatingpointTest.mul 27: [ OK ] SimdFloatingpointTest.mul (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzMul 27: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 27: [ RUN ] SimdFloatingpointTest.fma 27: [ OK ] SimdFloatingpointTest.fma (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzFma 27: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fms 27: [ OK ] SimdFloatingpointTest.fms (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnma 27: [ OK ] SimdFloatingpointTest.fnma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnms 27: [ OK ] SimdFloatingpointTest.fnms (0 ms) 27: [ RUN ] SimdFloatingpointTest.abs 27: [ OK ] SimdFloatingpointTest.abs (0 ms) 27: [ RUN ] SimdFloatingpointTest.neg 27: [ OK ] SimdFloatingpointTest.neg (0 ms) 27: [ RUN ] SimdFloatingpointTest.and 27: [ OK ] SimdFloatingpointTest.and (0 ms) 27: [ RUN ] SimdFloatingpointTest.or 27: [ OK ] SimdFloatingpointTest.or (0 ms) 27: [ RUN ] SimdFloatingpointTest.xor 27: [ OK ] SimdFloatingpointTest.xor (0 ms) 27: [ RUN ] SimdFloatingpointTest.andNot 27: [ OK ] SimdFloatingpointTest.andNot (0 ms) 27: [ RUN ] SimdFloatingpointTest.max 27: [ OK ] SimdFloatingpointTest.max (0 ms) 27: [ RUN ] SimdFloatingpointTest.min 27: [ OK ] SimdFloatingpointTest.min (0 ms) 27: [ RUN ] SimdFloatingpointTest.round 27: [ OK ] SimdFloatingpointTest.round (0 ms) 27: [ RUN ] SimdFloatingpointTest.roundMode 27: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 27: [ RUN ] SimdFloatingpointTest.trunc 27: [ OK ] SimdFloatingpointTest.trunc (0 ms) 27: [ RUN ] SimdFloatingpointTest.frexp 27: [ OK ] SimdFloatingpointTest.frexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.ldexp 27: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.rsqrt 27: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRsqrt 27: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.rcp 27: [ OK ] SimdFloatingpointTest.rcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRcp 27: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.selectByNotMask 27: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpNe 27: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLe 27: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLt 27: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 27: [ RUN ] SimdFloatingpointTest.testBits 27: [ OK ] SimdFloatingpointTest.testBits (0 ms) 27: [ RUN ] SimdFloatingpointTest.andB 27: [ OK ] SimdFloatingpointTest.andB (0 ms) 27: [ RUN ] SimdFloatingpointTest.orB 27: [ OK ] SimdFloatingpointTest.orB (0 ms) 27: [ RUN ] SimdFloatingpointTest.anyTrueB 27: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 27: [ RUN ] SimdFloatingpointTest.blend 27: [ OK ] SimdFloatingpointTest.blend (0 ms) 27: [ RUN ] SimdFloatingpointTest.reduce 27: [ OK ] SimdFloatingpointTest.reduce (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 27: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 27: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 27: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 27: 27: [----------] 16 tests from SimdFloatingpointUtilTest 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 27: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 27: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 27: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 27: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 27: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 27: [----------] 16 tests from SimdFloatingpointUtilTest (1 ms total) 27: 27: [----------] 3 tests from SimdVectorOperationsTest 27: [ RUN ] SimdVectorOperationsTest.iprod 27: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 27: [ RUN ] SimdVectorOperationsTest.norm2 27: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 27: [ RUN ] SimdVectorOperationsTest.cprod 27: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 27: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 27: 27: [----------] 56 tests from SimdMathTest 27: [ RUN ] SimdMathTest.generateTestPointsFloat 27: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 27: [ RUN ] SimdMathTest.copysign 27: [ OK ] SimdMathTest.copysign (0 ms) 27: [ RUN ] SimdMathTest.invsqrt 27: [ OK ] SimdMathTest.invsqrt (1 ms) 27: [ RUN ] SimdMathTest.maskzInvsqrt 27: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPair 27: [ OK ] SimdMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdMathTest.sqrt 27: [ OK ] SimdMathTest.sqrt (1 ms) 27: [ RUN ] SimdMathTest.sqrtUnsafe 27: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 27: [ RUN ] SimdMathTest.inv 27: [ OK ] SimdMathTest.inv (3 ms) 27: [ RUN ] SimdMathTest.maskzInv 27: [ OK ] SimdMathTest.maskzInv (0 ms) 27: [ RUN ] SimdMathTest.cbrt 27: [ OK ] SimdMathTest.cbrt (1 ms) 27: [ RUN ] SimdMathTest.invcbrt 27: [ OK ] SimdMathTest.invcbrt (9 ms) 27: [ RUN ] SimdMathTest.log2 27: [ OK ] SimdMathTest.log2 (1 ms) 27: [ RUN ] SimdMathTest.log 27: [ OK ] SimdMathTest.log (0 ms) 27: [ RUN ] SimdMathTest.exp2 27: [ OK ] SimdMathTest.exp2 (2 ms) 27: [ RUN ] SimdMathTest.exp2Unsafe 27: [ OK ] SimdMathTest.exp2Unsafe (9 ms) 27: [ RUN ] SimdMathTest.exp 27: [ OK ] SimdMathTest.exp (2 ms) 27: [ RUN ] SimdMathTest.expUnsafe 27: [ OK ] SimdMathTest.expUnsafe (1 ms) 27: [ RUN ] SimdMathTest.pow 27: [ OK ] SimdMathTest.pow (0 ms) 27: [ RUN ] SimdMathTest.powUnsafe 27: [ OK ] SimdMathTest.powUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erf 27: [ OK ] SimdMathTest.erf (9 ms) 27: [ RUN ] SimdMathTest.erfc 27: [ OK ] SimdMathTest.erfc (2 ms) 27: [ RUN ] SimdMathTest.sin 27: [ OK ] SimdMathTest.sin (1 ms) 27: [ RUN ] SimdMathTest.cos 27: [ OK ] SimdMathTest.cos (10 ms) 27: [ RUN ] SimdMathTest.tan 27: [ OK ] SimdMathTest.tan (1 ms) 27: [ RUN ] SimdMathTest.asin 27: [ OK ] SimdMathTest.asin (1 ms) 27: [ RUN ] SimdMathTest.acos 27: [ OK ] SimdMathTest.acos (1 ms) 27: [ RUN ] SimdMathTest.atan 27: [ OK ] SimdMathTest.atan (1 ms) 27: [ RUN ] SimdMathTest.atan2 27: [ OK ] SimdMathTest.atan2 (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrection 27: [ OK ] SimdMathTest.pmeForceCorrection (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrection 27: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (8 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracy 27: [ OK ] SimdMathTest.sqrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.invSingleAccuracy 27: [ OK ] SimdMathTest.invSingleAccuracy (3 ms) 27: [ RUN ] SimdMathTest.cbrtSingleAccuracy 27: [ OK ] SimdMathTest.cbrtSingleAccuracy (8 ms) 27: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 27: [ OK ] SimdMathTest.invcbrtSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.log2SingleAccuracy 27: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.logSingleAccuracy 27: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracy 27: [ OK ] SimdMathTest.exp2SingleAccuracy (10 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 27: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracy 27: [ OK ] SimdMathTest.expSingleAccuracy (3 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (8 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracy 27: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erfSingleAccuracy 27: [ OK ] SimdMathTest.erfSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.erfcSingleAccuracy 27: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.sinSingleAccuracy 27: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.cosSingleAccuracy 27: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.tanSingleAccuracy 27: [ OK ] SimdMathTest.tanSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.asinSingleAccuracy 27: [ OK ] SimdMathTest.asinSingleAccuracy (9 ms) 27: [ RUN ] SimdMathTest.acosSingleAccuracy 27: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atanSingleAccuracy 27: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atan2SingleAccuracy 27: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (1 ms) 27: [----------] 56 tests from SimdMathTest (122 ms total) 27: 27: [----------] 1 test from EmptyArrayRefTest 27: [ RUN ] EmptyArrayRefTest.IsEmpty 27: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 27: [----------] 1 test from EmptyArrayRefTest (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/1 (8 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/0.Assignment 27: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/1.Assignment 27: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/0.Basic 27: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/1.Basic 27: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/1 (1 ms total) 27: 27: [----------] 23 tests from SimdIntegerTest 27: [ RUN ] SimdIntegerTest.setZero 27: [ OK ] SimdIntegerTest.setZero (0 ms) 27: [ RUN ] SimdIntegerTest.set 27: [ OK ] SimdIntegerTest.set (0 ms) 27: [ RUN ] SimdIntegerTest.add 27: [ OK ] SimdIntegerTest.add (0 ms) 27: [ RUN ] SimdIntegerTest.sub 27: [ OK ] SimdIntegerTest.sub (0 ms) 27: [ RUN ] SimdIntegerTest.mul 27: [ OK ] SimdIntegerTest.mul (0 ms) 27: [ RUN ] SimdIntegerTest.and 27: [ OK ] SimdIntegerTest.and (0 ms) 27: [ RUN ] SimdIntegerTest.andNot 27: [ OK ] SimdIntegerTest.andNot (0 ms) 27: [ RUN ] SimdIntegerTest.or 27: [ OK ] SimdIntegerTest.or (0 ms) 27: [ RUN ] SimdIntegerTest.xor 27: [ OK ] SimdIntegerTest.xor (0 ms) 27: [ RUN ] SimdIntegerTest.extract 27: [ OK ] SimdIntegerTest.extract (0 ms) 27: [ RUN ] SimdIntegerTest.cvtR2I 27: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvttR2I 27: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvtI2R 27: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpLt 27: [ OK ] SimdIntegerTest.cmpLt (0 ms) 27: [ RUN ] SimdIntegerTest.testBits 27: [ OK ] SimdIntegerTest.testBits (0 ms) 27: [ RUN ] SimdIntegerTest.andB 27: [ OK ] SimdIntegerTest.andB (0 ms) 27: [ RUN ] SimdIntegerTest.orB 27: [ OK ] SimdIntegerTest.orB (0 ms) 27: [ RUN ] SimdIntegerTest.anyTrue 27: [ OK ] SimdIntegerTest.anyTrue (0 ms) 27: [ RUN ] SimdIntegerTest.blend 27: [ OK ] SimdIntegerTest.blend (0 ms) 27: [ RUN ] SimdIntegerTest.cvtB2IB 27: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 27: [ RUN ] SimdIntegerTest.cvtIB2B 27: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 27: [----------] 23 tests from SimdIntegerTest (0 ms total) 27: 27: [----------] 32 tests from Simd4FloatingpointTest 27: [ RUN ] Simd4FloatingpointTest.setZero 27: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 27: [ RUN ] Simd4FloatingpointTest.set 27: [ OK ] Simd4FloatingpointTest.set (0 ms) 27: [ RUN ] Simd4FloatingpointTest.add 27: [ OK ] Simd4FloatingpointTest.add (0 ms) 27: [ RUN ] Simd4FloatingpointTest.sub 27: [ OK ] Simd4FloatingpointTest.sub (0 ms) 27: [ RUN ] Simd4FloatingpointTest.mul 27: [ OK ] Simd4FloatingpointTest.mul (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fma 27: [ OK ] Simd4FloatingpointTest.fma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fms 27: [ OK ] Simd4FloatingpointTest.fms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnma 27: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnms 27: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.abs 27: [ OK ] Simd4FloatingpointTest.abs (0 ms) 27: [ RUN ] Simd4FloatingpointTest.neg 27: [ OK ] Simd4FloatingpointTest.neg (0 ms) 27: [ RUN ] Simd4FloatingpointTest.and 27: [ OK ] Simd4FloatingpointTest.and (0 ms) 27: [ RUN ] Simd4FloatingpointTest.or 27: [ OK ] Simd4FloatingpointTest.or (0 ms) 27: [ RUN ] Simd4FloatingpointTest.xor 27: [ OK ] Simd4FloatingpointTest.xor (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andNot 27: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 27: [ RUN ] Simd4FloatingpointTest.max 27: [ OK ] Simd4FloatingpointTest.max (0 ms) 27: [ RUN ] Simd4FloatingpointTest.min 27: [ OK ] Simd4FloatingpointTest.min (0 ms) 27: [ RUN ] Simd4FloatingpointTest.round 27: [ OK ] Simd4FloatingpointTest.round (0 ms) 27: [ RUN ] Simd4FloatingpointTest.trunc 27: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 27: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 27: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.selectByNotMask 27: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpNe 27: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLe 27: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLt 27: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andB 27: [ OK ] Simd4FloatingpointTest.andB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.orB 27: [ OK ] Simd4FloatingpointTest.orB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.anyTrue 27: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 27: [ RUN ] Simd4FloatingpointTest.blend 27: [ OK ] Simd4FloatingpointTest.blend (0 ms) 27: [ RUN ] Simd4FloatingpointTest.reduce 27: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 27: [ RUN ] Simd4FloatingpointTest.dotProduct 27: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 27: [ RUN ] Simd4FloatingpointTest.transpose 27: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 27: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 27: 27: [----------] 1 test from Simd4VectorOperationsTest 27: [ RUN ] Simd4VectorOperationsTest.norm2 27: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 27: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 27: 27: [----------] 2 tests from Simd4MathTest 27: [ RUN ] Simd4MathTest.invsqrt 27: [ OK ] Simd4MathTest.invsqrt (0 ms) 27: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 27: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 27: [----------] 2 tests from Simd4MathTest (0 ms total) 27: 27: [----------] 41 tests from SimdScalarTest 27: [ RUN ] SimdScalarTest.load 27: [ OK ] SimdScalarTest.load (0 ms) 27: [ RUN ] SimdScalarTest.loadU 27: [ OK ] SimdScalarTest.loadU (0 ms) 27: [ RUN ] SimdScalarTest.store 27: [ OK ] SimdScalarTest.store (0 ms) 27: [ RUN ] SimdScalarTest.storeU 27: [ OK ] SimdScalarTest.storeU (0 ms) 27: [ RUN ] SimdScalarTest.setZero 27: [ OK ] SimdScalarTest.setZero (0 ms) 27: [ RUN ] SimdScalarTest.andNot 27: [ OK ] SimdScalarTest.andNot (0 ms) 27: [ RUN ] SimdScalarTest.fma 27: [ OK ] SimdScalarTest.fma (0 ms) 27: [ RUN ] SimdScalarTest.fms 27: [ OK ] SimdScalarTest.fms (0 ms) 27: [ RUN ] SimdScalarTest.fnma 27: [ OK ] SimdScalarTest.fnma (0 ms) 27: [ RUN ] SimdScalarTest.fnms 27: [ OK ] SimdScalarTest.fnms (0 ms) 27: [ RUN ] SimdScalarTest.maskAdd 27: [ OK ] SimdScalarTest.maskAdd (0 ms) 27: [ RUN ] SimdScalarTest.maskzMul 27: [ OK ] SimdScalarTest.maskzMul (0 ms) 27: [ RUN ] SimdScalarTest.maskzFma 27: [ OK ] SimdScalarTest.maskzFma (0 ms) 27: [ RUN ] SimdScalarTest.abs 27: [ OK ] SimdScalarTest.abs (0 ms) 27: [ RUN ] SimdScalarTest.max 27: [ OK ] SimdScalarTest.max (0 ms) 27: [ RUN ] SimdScalarTest.min 27: [ OK ] SimdScalarTest.min (0 ms) 27: [ RUN ] SimdScalarTest.round 27: [ OK ] SimdScalarTest.round (0 ms) 27: [ RUN ] SimdScalarTest.trunc 27: [ OK ] SimdScalarTest.trunc (0 ms) 27: [ RUN ] SimdScalarTest.reduce 27: [ OK ] SimdScalarTest.reduce (0 ms) 27: [ RUN ] SimdScalarTest.testBits 27: [ OK ] SimdScalarTest.testBits (0 ms) 27: [ RUN ] SimdScalarTest.anyTrue 27: [ OK ] SimdScalarTest.anyTrue (0 ms) 27: [ RUN ] SimdScalarTest.selectByMask 27: [ OK ] SimdScalarTest.selectByMask (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMask 27: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 27: [ RUN ] SimdScalarTest.blend 27: [ OK ] SimdScalarTest.blend (0 ms) 27: [ RUN ] SimdScalarTest.cvtR2I 27: [ OK ] SimdScalarTest.cvtR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvttR2I 27: [ OK ] SimdScalarTest.cvttR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvtI2R 27: [ OK ] SimdScalarTest.cvtI2R (0 ms) 27: [ RUN ] SimdScalarTest.cvtF2D 27: [ OK ] SimdScalarTest.cvtF2D (0 ms) 27: [ RUN ] SimdScalarTest.cvtD2D 27: [ OK ] SimdScalarTest.cvtD2D (0 ms) 27: [ RUN ] SimdScalarTest.loadI 27: [ OK ] SimdScalarTest.loadI (0 ms) 27: [ RUN ] SimdScalarTest.loadUI 27: [ OK ] SimdScalarTest.loadUI (0 ms) 27: [ RUN ] SimdScalarTest.storeI 27: [ OK ] SimdScalarTest.storeI (0 ms) 27: [ RUN ] SimdScalarTest.storeUI 27: [ OK ] SimdScalarTest.storeUI (0 ms) 27: [ RUN ] SimdScalarTest.andNotI 27: [ OK ] SimdScalarTest.andNotI (0 ms) 27: [ RUN ] SimdScalarTest.testBitsI 27: [ OK ] SimdScalarTest.testBitsI (0 ms) 27: [ RUN ] SimdScalarTest.selectByMaskI 27: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMaskI 27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 27: [ RUN ] SimdScalarTest.blendI 27: [ OK ] SimdScalarTest.blendI (0 ms) 27: [ RUN ] SimdScalarTest.cvtB2IB 27: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 27: [ RUN ] SimdScalarTest.cvtIB2B 27: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 27: [ RUN ] SimdScalarTest.expandScalarsToTriplets 27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 27: [----------] 41 tests from SimdScalarTest (1 ms total) 27: 27: [----------] 8 tests from SimdScalarUtilTest 27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 27: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 27: 27: [----------] 37 tests from SimdScalarMathTest 27: [ RUN ] SimdScalarMathTest.copysign 27: [ OK ] SimdScalarMathTest.copysign (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPair 27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdScalarMathTest.inv 27: [ OK ] SimdScalarMathTest.inv (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrt 27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdScalarMathTest.log 27: [ OK ] SimdScalarMathTest.log (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2 27: [ OK ] SimdScalarMathTest.exp2 (0 ms) 27: [ RUN ] SimdScalarMathTest.exp 27: [ OK ] SimdScalarMathTest.exp (0 ms) 27: [ RUN ] SimdScalarMathTest.erf 27: [ OK ] SimdScalarMathTest.erf (0 ms) 27: [ RUN ] SimdScalarMathTest.erfc 27: [ OK ] SimdScalarMathTest.erfc (0 ms) 27: [ RUN ] SimdScalarMathTest.sincos 27: [ OK ] SimdScalarMathTest.sincos (0 ms) 27: [ RUN ] SimdScalarMathTest.sin 27: [ OK ] SimdScalarMathTest.sin (0 ms) 27: [ RUN ] SimdScalarMathTest.cos 27: [ OK ] SimdScalarMathTest.cos (0 ms) 27: [ RUN ] SimdScalarMathTest.tan 27: [ OK ] SimdScalarMathTest.tan (0 ms) 27: [ RUN ] SimdScalarMathTest.asin 27: [ OK ] SimdScalarMathTest.asin (0 ms) 27: [ RUN ] SimdScalarMathTest.acos 27: [ OK ] SimdScalarMathTest.acos (0 ms) 27: [ RUN ] SimdScalarMathTest.atan 27: [ OK ] SimdScalarMathTest.atan (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2 27: [ OK ] SimdScalarMathTest.atan2 (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrection 27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.invSingleAccuracy 27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.logSingleAccuracy 27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.expSingleAccuracy 27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 27: [----------] 37 tests from SimdScalarMathTest (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 288 tests from 22 test cases ran. (133 ms total) 27: [ PASSED ] 288 tests. 27/30 Test #27: SimdUnitTests .................... Passed 0.22 sec test 28 Start 28: CompatibilityHelpersTests 28: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/CompatibilityHelpersTests.xml" 28: Test timeout computed to be: 30 28: [==========] Running 170 tests from 12 test cases. 28: [----------] Global test environment set-up. 28: [----------] 45 tests from OptionalTest 28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes 28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructEmpty 28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms) 28: [ RUN ] OptionalTest.CanConstructFromNullopt 28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType 28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (1 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral 28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting 28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValue 28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting 28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValue 28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral 28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage 28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral 28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromValue 28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignFromValue 28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanResetContent 28: [ OK ] OptionalTest.CanResetContent (0 ms) 28: [ RUN ] OptionalTest.ProvidesRelationalOperators 28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators 28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.CanProduceHash 28: [ OK ] OptionalTest.CanProduceHash (0 ms) 28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType 28: alignment_of: 1 28: alignment_of: 2 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 16 28: alignment_of: 1 28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms) 28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType 28: sizeof( nonstd::optional_lite::detail::storage_t ): 1 28: sizeof( optional ): 2 (1) 28: sizeof( optional ): 4 (2) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 32 (16) 28: sizeof( optional ): 2 (1) 28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms) 28: [----------] 45 tests from OptionalTest (1 ms total) 28: 28: [----------] 7 tests from MakeOptionalTest 28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] MakeOptionalTest.CanCopyConstruct 28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanMoveConstruct 28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms) 28: [----------] 7 tests from MakeOptionalTest (0 ms total) 28: 28: [----------] 4 tests from OptionalMemberSwapTest 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms) 28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total) 28: 28: [----------] 4 tests from OptionalImplicitValueTest 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms) 28: [----------] 4 tests from OptionalImplicitValueTest (1 ms total) 28: 28: [----------] 20 tests from OptionalIntValueTest 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool 28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms) 28: [----------] 20 tests from OptionalIntValueTest (0 ms total) 28: 28: [----------] 1 test from NotNullConstruction 28: [ RUN ] NotNullConstruction.Works 28: [ OK ] NotNullConstruction.Works (0 ms) 28: [----------] 1 test from NotNullConstruction (0 ms total) 28: 28: [----------] 1 test from NotNullCasting 28: [ RUN ] NotNullCasting.Works 28: [ OK ] NotNullCasting.Works (0 ms) 28: [----------] 1 test from NotNullCasting (0 ms total) 28: 28: [----------] 1 test from NotNullAssignment 28: [ RUN ] NotNullAssignment.Works 28: [ OK ] NotNullAssignment.Works (0 ms) 28: [----------] 1 test from NotNullAssignment (0 ms total) 28: 28: [----------] 1 test from MakeNotNull 28: [ RUN ] MakeNotNull.Works 28: [ OK ] MakeNotNull.Works (0 ms) 28: [----------] 1 test from MakeNotNull (0 ms total) 28: 28: [----------] 1 test from NotNull 28: [ RUN ] NotNull.WorksInContainers 28: [ OK ] NotNull.WorksInContainers (0 ms) 28: [----------] 1 test from NotNull (0 ms total) 28: 28: [----------] 80 tests from StringViewTest 28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView 28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize 28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromCString 28: [ OK ] StringViewTest.CanConstructFromCString (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.AllowForwardIteration 28: [ OK ] StringViewTest.AllowForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstForwardIteration 28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowReverseIteration 28: [ OK ] StringViewTest.AllowReverseIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstReverseIteration 28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms) 28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize 28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms) 28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty 28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex 28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaAt 28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms) 28: [ RUN ] StringViewTest.CanAccessAllElementsViaData 28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms) 28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr 28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms) 28: [ RUN ] StringViewTest.CanRemovePrefix 28: [ OK ] StringViewTest.CanRemovePrefix (0 ms) 28: [ RUN ] StringViewTest.CanRemoveSuffix 28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms) 28: [ RUN ] StringViewTest.CanSwapWithOtherView 28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms) 28: [ RUN ] StringViewTest.CanCopySubstringWithCopy 28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms) 28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr 28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms) 28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare 28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare 28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCompareToViews 28: [ OK ] StringViewTest.CanCompareToViews (0 ms) 28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView 28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms) 28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual 28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms) 28: [ RUN ] StringViewTest.CanPrintViewToPutputStream 28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms) 28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms) 28: [----------] 80 tests from StringViewTest (1 ms total) 28: 28: [----------] 5 tests from StringViewExtensionTest 28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString 28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms) 28: [----------] 5 tests from StringViewExtensionTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 170 tests from 12 test cases ran. (8 ms total) 28: [ PASSED ] 170 tests. 28/30 Test #28: CompatibilityHelpersTests ........ Passed 0.07 sec test 29 Start 29: FileIOTests 29: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/FileIOTests.xml" 29: Test timeout computed to be: 30 29: [==========] Running 33 tests from 8 test cases. 29: [----------] Global test environment set-up. 29: [----------] 2 tests from FileMD5Test 29: [ RUN ] FileMD5Test.CanComputeMD5 29: [ OK ] FileMD5Test.CanComputeMD5 (5 ms) 29: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 29: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 29: [----------] 2 tests from FileMD5Test (5 ms total) 29: 29: [----------] 3 tests from MrcSerializer 29: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 29: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 29: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 29: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 29: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 29: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (1 ms) 29: [----------] 3 tests from MrcSerializer (1 ms total) 29: 29: [----------] 4 tests from MrcDensityMap 29: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 29: [ OK ] MrcDensityMap.RoundTripIsIdempotent (1 ms) 29: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 29: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 29: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 29: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 29: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 29: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 29: [----------] 4 tests from MrcDensityMap (2 ms total) 29: 29: [----------] 8 tests from MrcDensityMapHeaderTest 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 29: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 29: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 29: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (4 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.IsSane 29: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 29: [----------] 8 tests from MrcDensityMapHeaderTest (4 ms total) 29: 29: [----------] 9 tests from ReadTest 29: [ RUN ] ReadTest.get_eint_ReadsInteger 29: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side '0.8' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint_WarnsAboutFloat (1 ms) 29: [ RUN ] ReadTest.get_eint_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 29: [ RUN ] ReadTest.get_eint64_ReadsInteger 29: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side '0.8' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 29: [ RUN ] ReadTest.get_eint64_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 29: [ RUN ] ReadTest.get_ereal_ReadsInteger 29: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_ereal_ReadsFloat 29: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 29: [ RUN ] ReadTest.get_ereal_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not a 29: real value 29: 29: 29: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 29: [----------] 9 tests from ReadTest (1 ms total) 29: 29: [----------] 1 test from FileIOXdrSerializerTest 29: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 29: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 29: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 29: 29: [----------] 2 tests from TngTest 29: [ RUN ] TngTest.CanOpenTngFile 29: TNG library: Cannot open file spc2-traj.tng. /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c: 890 29: TNG library: Cannot open file spc2-traj.tng. /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c: 890 29: [ OK ] TngTest.CanOpenTngFile (0 ms) 29: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 29: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 29: [----------] 2 tests from TngTest (0 ms total) 29: 29: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (1 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 29: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (2 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 33 tests from 8 test cases ran. (15 ms total) 29: [ PASSED ] 33 tests. 29/30 Test #29: FileIOTests ...................... Passed 0.07 sec test 30 Start 30: SelectionUnitTests 30: Test command: /build/reproducible-path/gromacs-2020.6/build/mpich/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/mpich/Testing/Temporary/SelectionUnitTests.xml" 30: Test timeout computed to be: 30 30: [==========] Running 192 tests from 11 test cases. 30: [----------] Global test environment set-up. 30: [----------] 1 test from IndexGroupTest 30: [ RUN ] IndexGroupTest.RemovesDuplicates 30: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 30: [----------] 1 test from IndexGroupTest (0 ms total) 30: 30: [----------] 15 tests from IndexBlockTest 30: [ RUN ] IndexBlockTest.CreatesUnknownBlock 30: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 30: [ RUN ] IndexBlockTest.CreatesAtomBlock 30: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 30: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 30: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 30: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 30: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (1 ms) 30: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 30: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesSingleBlock 30: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 30: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 30: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 30: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 30: [----------] 15 tests from IndexBlockTest (1 ms total) 30: 30: [----------] 11 tests from IndexMapTest 30: [ RUN ] IndexMapTest.InitializesAtomBlock 30: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 30: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 30: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 30: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 30: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 30: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 30: [ RUN ] IndexMapTest.InitializesMoleculeBlock 30: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 30: [ RUN ] IndexMapTest.MapsSingleBlock 30: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 30: [ RUN ] IndexMapTest.MapsResidueBlocks 30: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms) 30: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 30: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 30: [ RUN ] IndexMapTest.HandlesMultipleRequests 30: [ OK ] IndexMapTest.HandlesMultipleRequests (8 ms) 30: [----------] 11 tests from IndexMapTest (10 ms total) 30: 30: [----------] 3 tests from IndexGroupsAndNamesTest 30: [ RUN ] IndexGroupsAndNamesTest.containsNames 30: [ OK ] IndexGroupsAndNamesTest.containsNames (1 ms) 30: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 30: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 30: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 30: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 30: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total) 30: 30: [----------] 15 tests from NeighborhoodSearchTest 30: [ RUN ] NeighborhoodSearchTest.SimpleSearch 30: [ OK ] NeighborhoodSearchTest.SimpleSearch (22 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 30: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (34 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchBox 30: [ OK ] NeighborhoodSearchTest.GridSearchBox (3 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 30: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (21 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 30: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (9 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 30: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 30: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (6 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 30: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 30: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (82 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 30: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 30: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 30: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 30: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 30: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (7 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 30: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 30: [----------] 15 tests from NeighborhoodSearchTest (186 ms total) 30: 30: [----------] 12 tests from PositionCalculationTest 30: [ RUN ] PositionCalculationTest.ComputesAtomPositions 30: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 30: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 30: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 30: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 30: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 30: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (4 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 30: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionMask 30: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 30: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 30: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 30: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 30: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms) 30: [----------] 12 tests from PositionCalculationTest (7 ms total) 30: 30: [----------] 29 tests from SelectionCollectionTest 30: [ RUN ] SelectionCollectionTest.HandlesNoSelections 30: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 30: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 30: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 30: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 30: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 30: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 30: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 30: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (4 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 30: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 30: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 30: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 30: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (4 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 30: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 30: [----------] 29 tests from SelectionCollectionTest (17 ms total) 30: 30: [----------] 14 tests from SelectionCollectionInteractiveTest 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 30: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (5 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 30: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 30: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 30: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 30: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 30: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (4 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms) 30: [----------] 14 tests from SelectionCollectionInteractiveTest (14 ms total) 30: 30: [----------] 66 tests from SelectionCollectionDataTest 30: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 30: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 30: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResnr 30: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 30: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 30: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 30: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 30: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 30: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (5 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesChain 30: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMass 30: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesCharge 30: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 30: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 30: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 30: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBeta 30: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResname 30: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 30: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 30: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (9 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (4 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (6 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 30: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (2 ms) 30: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 30: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 30: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 30: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 30: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 30: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 30: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 30: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 30: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (5 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 30: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 30: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 30: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 30: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (4 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 30: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 30: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 30: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 30: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 30: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 30: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (8 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 30: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 30: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 30: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 30: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 30: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 30: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 30: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 30: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 30: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (5 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 30: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 30: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 30: [----------] 66 tests from SelectionCollectionDataTest (102 ms total) 30: 30: [----------] 17 tests from SelectionOptionTest 30: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 30: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 30: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms) 30: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 30: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 30: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 30: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms) 30: [ RUN ] SelectionOptionTest.ChecksEmptySelections 30: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 30: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 30: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooManySelections 30: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 30: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms) 30: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 30: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesAdjuster 30: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 30: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 30: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 30: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 30: [----------] 17 tests from SelectionOptionTest (4 ms total) 30: 30: [----------] 9 tests from SelectionFileOptionTest 30: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 30: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 30: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 30: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 30: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 30: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 30: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (9 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 30: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 30: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 30: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 30: [----------] 9 tests from SelectionFileOptionTest (10 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 192 tests from 11 test cases ran. (352 ms total) 30: [ PASSED ] 192 tests. 30/30 Test #30: SelectionUnitTests ............... Passed 0.41 sec 100% tests passed, 0 tests failed out of 30 Label Time Summary: GTest = 5.87 sec*proc (30 tests) MpiTest = 1.64 sec*proc (3 tests) UnitTest = 5.87 sec*proc (30 tests) Total Test time (real) = 5.91 sec touch build-mpich dh_testdir /usr/bin/make -j16 -C build/openmpi make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/openmpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/openmpi/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/openmpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' Scanning dependencies of target scanner /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' Scanning dependencies of target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/parser.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' Scanning dependencies of target thread_mpi cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/openmpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/openmpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/mdrun.cpp Scanning dependencies of target modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/dict.c make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 1%] Built target thread_mpi cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/energyelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/modularsimulator.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 1%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/shellfcelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/vrescalethermostat.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 2%] Built target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 2%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 5%] Built target tng_io_obj make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2020.6/build/openmpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H 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&& /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/qm_gaussian.cpp /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem 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-fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program.cpp /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H 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/build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= Scanning dependencies of target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' Scanning dependencies of target lmfit_objlib /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/parser.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/lmfit/lmmin.cpp Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' Scanning dependencies of target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/mdrun.cpp [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c Scanning dependencies of target modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/coder.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [ 1%] Built target thread_mpi cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong 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/build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/energyelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong 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/build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat 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CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/shellfcelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator/vrescalethermostat.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [ 2%] Built target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [ 2%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [ 5%] Built target tng_io_obj make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd 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/build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include 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/build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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/build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem 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/build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/qm_mopac.cpp /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src 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CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/lmfit -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_solve.cpp /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem 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'/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi 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'/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 0%] 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make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 1%] Built target thread_mpi make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 1%] Built target release-version-info [ 1%] Built target lmfit_objlib [ 3%] Built target tng_io_obj [ 3%] Built target linearalgebra /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/gtest /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color= [ 5%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend Scanning dependencies of target gtest make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/gtest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src 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/build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 72%] Built target libgromacs cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/gtest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../../lib/libgtest.a CMakeFiles/gtest.dir/src/gtest-all.cc.o /usr/bin/ranlib ../../../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 72%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= Scanning dependencies of target gmock make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -D_GNU_SOURCE=1 -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmock.a CMakeFiles/gmock.dir/src/gmock-all.cc.o /usr/bin/ranlib ../../../../lib/libgmock.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 73%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/testutils /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils 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/build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/cmdlinetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem 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CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 76%] Built target testutils /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-mpi-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fft/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/mpitest.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp Scanning dependencies of target testutils-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend Scanning dependencies of target onlinehelp-test-shared cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/interactivetest.cpp Scanning dependencies of target domdec-test make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/mock_helptopic.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build Scanning dependencies of target applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests/hashedmap.cpp Scanning dependencies of target fft-test make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfitting.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' Scanning dependencies of target gpu_utils-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fft/tests/fft.cpp Scanning dependencies of target selection-test make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/gputest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' Scanning dependencies of target ewald-test make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/hardware/tests/hardwaretopology.cpp /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' Scanning dependencies of target utility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/indexutil.cpp /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/alignedallocator.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmebsplinetest.cpp Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build Scanning dependencies of target math-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/calc_verletbuf.cpp /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/refdata_tests.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/arrayref.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 77%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constr.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 77%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdspan-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 77%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmegathertest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 77%] Built target hardware-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 78%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= Scanning dependencies of target pbcutil-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pbcutil/tests/pbcenums.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/coordinatetransformation.cpp [ 78%] Built target fft-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/exponentialdistribution.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 78%] Built target domdec-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 78%] Built target pbcutil-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/tables/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a Scanning dependencies of target table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask32.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 78%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 78%] Built target testutils-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/tests/usergpuids.cpp Scanning dependencies of target topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/tests/testhardwarecontexts.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 79%] Built target taskassignment-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/pulling/tests/pull.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 80%] Built target topology-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 80%] Built target applied_forces-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/optionsassigner.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 81%] Built target pull-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/optional.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/tests/devicetransfers.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 82%] Built target ewald-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/confio.cpp /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 82%] Built target mdspan-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/defaultinitializationallocator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 82%] Built target table-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/functions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 82%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/awh/tests/grid.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 82%] Built target mdrunutility-mpi-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp [ 83%] Built target awh-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymap.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 83%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/tests/string_view.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 84%] Built target selection-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settle.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 85%] Built target onlinehelp-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/multidimarray.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 86%] Built target random-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd 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CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/simulationsignal.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 87%] Built target options-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/tests/updategroupscog.cpp cd 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CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat 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/build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 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-fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 88%] Built target fileio-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/scalar_math.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 89%] Built target compat-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/reproducible-path/gromacs-2020.6/build/openmpi/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2020.6/src/external -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 90%] Built target commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 92%] Built target mdlib-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 94%] Built target simd-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 97%] Built target utility-test cd /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [100%] Built target math-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/openmpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' (cd build/openmpi ; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2020.6/build/openmpi/lib \ OMPI_MCA_plm_rsh_agent=/bin/false \ OMPI_MCA_rmaps_base_oversubscribe=1 \ ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 ) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2020.6/build/openmpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2020.6/build/openmpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2020.6/build/openmpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2020.6/build/openmpi/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2020.6/build/openmpi Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (2 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (4 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnys 1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (22 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms) 1: [----------] 34 tests from ReferenceDataTest (33 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (0 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (3 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (4 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (39 ms total) 1: [ PASSED ] 59 tests. 1/30 Test #1: TestUtilsUnitTests ............... Passed 5.42 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.openmpi "-np" "2" "-host" "localhost" "/build/reproducible-path/gromacs-2020.6/build/openmpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (2 ms) 2: [----------] 1 test from MpiSelfTest (11 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (11 ms total) 2: [ PASSED ] 1 test. 2/30 Test #2: TestUtilsMpiUnitTests ............ Passed 1.56 sec test 3 Start 3: UtilityUnitTests 3: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/UtilityUnitTests.xml" 3: Test timeout computed to be: 30 3: [==========] Running 347 tests from 56 test cases. 3: [----------] Global test environment set-up. 3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.Move 3: [ OK ] AllocatorTest/0.Move (0 ms) 3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/0 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.Move 3: [ OK ] AllocatorTest/1.Move (0 ms) 3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/1 (1 ms total) 3: 3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.Move 3: [ OK ] AllocatorTest/2.Move (0 ms) 3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/2 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.Move 3: [ OK ] AllocatorTest/3.Move (0 ms) 3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/3 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.Move 3: [ OK ] AllocatorTest/4.Move (0 ms) 3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/4 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/5.Move 3: [ OK ] AllocatorTest/5.Move (0 ms) 3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/5 (1 ms total) 3: 3: [----------] 1 test from AllocatorUntypedTest 3: [ RUN ] AllocatorUntypedTest.Comparison 3: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 3: [----------] 1 test from AllocatorUntypedTest (0 ms total) 3: 3: [----------] 1 test from EmptyArrayRefTest 3: [ RUN ] EmptyArrayRefTest.IsEmpty 3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyArrayRefTest (0 ms total) 3: 3: [----------] 1 test from EmptyConstArrayRefTest 3: [ RUN ] EmptyConstArrayRefTest.IsEmpty 3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/14 (1 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 3: 3: [----------] 2 tests from CStringUtilityTest 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 3: [----------] 2 tests from CStringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from DefaultInitializationAllocator 3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 3: 3: [----------] 4 tests from EnumerationHelpersTest 3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 3: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 3: 3: [----------] 9 tests from FixedCapacityVectorTest 3: [ RUN ] FixedCapacityVectorTest.IsEmpty 3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PushWorks 3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PopWorks 3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ClearWorks 3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.AtThrows 3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 3: [ RUN ] FixedCapacityVectorTest.IteratorWorks 3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 3: 3: [----------] 5 tests from InMemorySerializerTest 3: [ RUN ] InMemorySerializerTest.Roundtrip 3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SizeIsCorrect 3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 3: [----------] 5 tests from InMemorySerializerTest (0 ms total) 3: 3: [----------] 4 tests from KeyValueTreeSerializerTest 3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (23 ms) 3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (8 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (8 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 3: [----------] 4 tests from KeyValueTreeSerializerTest (39 ms total) 3: 3: [----------] 6 tests from TreeValueTransformTest 3: [ RUN ] TreeValueTransformTest.SimpleTransforms 3: [ OK ] TreeValueTransformTest.SimpleTransforms (8 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (2 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromString 3: [ OK ] TreeValueTransformTest.ObjectFromString (6 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms) 3: [ RUN ] TreeValueTransformTest.ScopedTransformRules 3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 3: [----------] 6 tests from TreeValueTransformTest (17 ms total) 3: 3: [----------] 1 test from TreeValueTransformErrorTest 3: [ RUN ] TreeValueTransformErrorTest.ConversionError 3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 3: 3: [----------] 7 tests from LoggerTest 3: [ RUN ] LoggerTest.EmptyLoggerWorks 3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToStream 3: [ OK ] LoggerTest.LogsToStream (0 ms) 3: [ RUN ] LoggerTest.LogsToFile 3: [ OK ] LoggerTest.LogsToFile (0 ms) 3: [ RUN ] LoggerTest.LevelFilteringWorks 3: [ OK ] LoggerTest.LevelFilteringWorks (1 ms) 3: [ RUN ] LoggerTest.LogsToMultipleStreams 3: [ OK ] LoggerTest.LogsToMultipleStreams (1 ms) 3: [ RUN ] LoggerTest.LogsToMultipleFiles 3: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 3: [ RUN ] LoggerTest.LogsToStreamAndFile 3: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 3: [----------] 7 tests from LoggerTest (2 ms total) 3: 3: [----------] 4 tests from MutexBasicTest 3: [ RUN ] MutexBasicTest.CanBeMade 3: [ OK ] MutexBasicTest.CanBeMade (0 ms) 3: [ RUN ] MutexBasicTest.CanBeLocked 3: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeTryLocked 3: [ OK ] MutexBasicTest.CanBeTryLocked (1 ms) 3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 3: [----------] 4 tests from MutexBasicTest (1 ms total) 3: 3: [----------] 3 tests from MutexTaskTest 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (12 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (8 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 3: [----------] 3 tests from MutexTaskTest (20 ms total) 3: 3: [----------] 2 tests from PathTest 3: [ RUN ] PathTest.StripSourcePrefixWorks 3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 3: [ RUN ] PathTest.SearchOperationsWork 3: [ OK ] PathTest.SearchOperationsWork (1 ms) 3: [----------] 2 tests from PathTest (1 ms total) 3: 3: [----------] 2 tests from PhysicalNodeCommunicatorTest 3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 3: 3: [----------] 9 tests from StringUtilityTest 3: [ RUN ] StringUtilityTest.StartsWith 3: [ OK ] StringUtilityTest.StartsWith (0 ms) 3: [ RUN ] StringUtilityTest.EndsWith 3: [ OK ] StringUtilityTest.EndsWith (0 ms) 3: [ RUN ] StringUtilityTest.StripSuffixIfPresent 3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 3: [ RUN ] StringUtilityTest.StripString 3: [ OK ] StringUtilityTest.StripString (0 ms) 3: [ RUN ] StringUtilityTest.SplitString 3: [ OK ] StringUtilityTest.SplitString (0 ms) 3: [ RUN ] StringUtilityTest.SplitDelimitedString 3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 3: [----------] 9 tests from StringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from FormatStringTest 3: [ RUN ] FormatStringTest.HandlesBasicFormatting 3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 3: [ RUN ] FormatStringTest.HandlesLongStrings 3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 3: [----------] 2 tests from FormatStringTest (0 ms total) 3: 3: [----------] 1 test from StringFormatterTest 3: [ RUN ] StringFormatterTest.HandlesBasicFormatting 3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 3: [----------] 1 test from StringFormatterTest (0 ms total) 3: 3: [----------] 1 test from formatAndJoinTest 3: [ RUN ] formatAndJoinTest.Works 3: [ OK ] formatAndJoinTest.Works (0 ms) 3: [----------] 1 test from formatAndJoinTest (0 ms total) 3: 3: [----------] 1 test from JoinStringsTest 3: [ RUN ] JoinStringsTest.Works 3: [ OK ] JoinStringsTest.Works (0 ms) 3: [----------] 1 test from JoinStringsTest (0 ms total) 3: 3: [----------] 6 tests from ReplaceAllTest 3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesNoMatches 3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 3: [----------] 6 tests from ReplaceAllTest (1 ms total) 3: 3: [----------] 10 tests from TextLineWrapperTest 3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectly 3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndent 3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (3 ms) 3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 3: [----------] 10 tests from TextLineWrapperTest (3 ms total) 3: 3: [----------] 6 tests from TextWriterTest 3: [ RUN ] TextWriterTest.WritesLines 3: [ OK ] TextWriterTest.WritesLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInParts 3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 3: [ RUN ] TextWriterTest.WritesWrappedLines 3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 3: [ RUN ] TextWriterTest.TracksNewlines 3: [ OK ] TextWriterTest.TracksNewlines (0 ms) 3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 3: [----------] 6 tests from TextWriterTest (1 ms total) 3: 3: [----------] 1 test from TypeTraitsTest 3: [ RUN ] TypeTraitsTest.IsIntegralConstant 3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 3: [----------] 1 test from TypeTraitsTest (0 ms total) 3: 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 3: 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (11 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (7 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (4 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (9 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (16 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (17 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (64 ms total) 3: 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 347 tests from 56 test cases ran. (161 ms total) 3: [ PASSED ] 347 tests. 3/30 Test #3: UtilityUnitTests ................. Passed 1.43 sec test 4 Start 4: UtilityMpiUnitTests 4: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "-host" "localhost" "/build/reproducible-path/gromacs-2020.6/build/openmpi/bin/utility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/UtilityMpiUnitTests.xml" 4: Test timeout computed to be: 30 4: [==========] Running 2 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from PhysicalNodeCommunicatorTest 4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (16 ms) 4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (11 ms) 4: [----------] 2 tests from PhysicalNodeCommunicatorTest (28 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test case ran. (28 ms total) 4: [ PASSED ] 2 tests. 4/30 Test #4: UtilityMpiUnitTests .............. Passed 1.53 sec test 5 Start 5: MdlibUnitTest 5: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/MdlibUnitTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 187 tests from 13 test cases. 5: [----------] Global test environment set-up. 5: [----------] 1 test from VerletBufferConstraintTest 5: [ RUN ] VerletBufferConstraintTest.EqualMasses 5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 5: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 5: 5: [----------] 2 tests from PrEbinTest 5: [ RUN ] PrEbinTest.HandlesAverages 5: [ OK ] PrEbinTest.HandlesAverages (22 ms) 5: [ RUN ] PrEbinTest.HandlesEmptyAverages 5: [ OK ] PrEbinTest.HandlesEmptyAverages (12 ms) 5: [----------] 2 tests from PrEbinTest (34 ms total) 5: 5: [----------] 4 tests from ShakeTest 5: [ RUN ] ShakeTest.ConstrainsOneBond 5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 5: [----------] 4 tests from ShakeTest (0 ms total) 5: 5: [----------] 1 test from NullSignalTest 5: [ RUN ] NullSignalTest.NullSignallerWorks 5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 5: [----------] 1 test from NullSignalTest (0 ms total) 5: 5: [----------] 7 tests from SignalTest 5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 5: [----------] 7 tests from SignalTest (0 ms total) 5: 5: [----------] 9 tests from UpdateGroups 5: [ RUN ] UpdateGroups.ethaneUA 5: [ OK ] UpdateGroups.ethaneUA (0 ms) 5: [ RUN ] UpdateGroups.methane 5: [ OK ] UpdateGroups.methane (0 ms) 5: [ RUN ] UpdateGroups.ethane 5: [ OK ] UpdateGroups.ethane (0 ms) 5: [ RUN ] UpdateGroups.butaneUA 5: [ OK ] UpdateGroups.butaneUA (0 ms) 5: [ RUN ] UpdateGroups.waterThreeSite 5: [ OK ] UpdateGroups.waterThreeSite (0 ms) 5: [ RUN ] UpdateGroups.waterFourSite 5: [ OK ] UpdateGroups.waterFourSite (0 ms) 5: [ RUN ] UpdateGroups.fourAtomsWithSettle 5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 5: [ RUN ] UpdateGroups.waterFlexAngle 5: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 5: [ RUN ] UpdateGroups.twoMoltypes 5: [ OK ] UpdateGroups.twoMoltypes (0 ms) 5: [----------] 9 tests from UpdateGroups (0 ms total) 5: 5: [----------] 1 test from UpdateGroupsCog 5: [ RUN ] UpdateGroupsCog.ComputesCogs 5: [ OK ] UpdateGroupsCog.ComputesCogs (12 ms) 5: [----------] 1 test from UpdateGroupsCog (12 ms total) 5: 5: [----------] 84 tests from WithParameters/ConstraintsTest 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms) 5: [----------] 84 tests from WithParameters/ConstraintsTest (3 ms total) 5: 5: [----------] 11 tests from WithParameters/EnergyOutputTest 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (25 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (20 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (16 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 5: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (60 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (20 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (7 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (20 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (19 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (15 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 5: Opened /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (20 ms) 5: [----------] 11 tests from WithParameters/EnergyOutputTest (231 ms total) 5: 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (5 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (5 ms total) 5: 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (1 ms total) 5: 5: [----------] 16 tests from WithParameters/LeapFrogTest 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (8 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (4 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (31 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (10 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (20 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (24 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (15 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (8 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (11 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (20 ms) 5: [----------] 16 tests from WithParameters/LeapFrogTest (157 ms total) 5: 5: [----------] 13 tests from WithParameters/SettleTest 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (5 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (12 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (2 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (5 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 5: [----------] 13 tests from WithParameters/SettleTest (28 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 187 tests from 13 test cases ran. (472 ms total) 5: [ PASSED ] 187 tests. 5/30 Test #5: MdlibUnitTest .................... Passed 1.67 sec test 6 Start 6: AppliedForcesUnitTest 6: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/AppliedForcesUnitTest.xml" 6: Test timeout computed to be: 30 6: [==========] Running 20 tests from 4 test cases. 6: [----------] Global test environment set-up. 6: [----------] 2 tests from DensityFittingTest 6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 6: [ RUN ] DensityFittingTest.SingleAtom 6: [ OK ] DensityFittingTest.SingleAtom (42 ms) 6: [----------] 2 tests from DensityFittingTest (42 ms total) 6: 6: [----------] 8 tests from DensityFittingOptionsTest 6: [ RUN ] DensityFittingOptionsTest.DefaultParameters 6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 6: [ RUN ] DensityFittingOptionsTest.KvtToInternal 6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 6: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 6: 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest 6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 6: 6: [----------] 3 tests from ElectricFieldTest 6: [ RUN ] ElectricFieldTest.Static 6: [ OK ] ElectricFieldTest.Static (5 ms) 6: [ RUN ] ElectricFieldTest.Oscillating 6: [ OK ] ElectricFieldTest.Oscillating (1 ms) 6: [ RUN ] ElectricFieldTest.Pulsed 6: [ OK ] ElectricFieldTest.Pulsed (0 ms) 6: [----------] 3 tests from ElectricFieldTest (6 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 20 tests from 4 test cases ran. (49 ms total) 6: [ PASSED ] 20 tests. 6/30 Test #6: AppliedForcesUnitTest ............ Passed 1.25 sec test 7 Start 7: CommandLineUnitTests 7: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/CommandLineUnitTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 59 tests from 7 test cases. 7: [----------] Global test environment set-up. 7: [----------] 3 tests from CommandLineHelpModuleTest 7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (12 ms) 7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (8 ms) 7: [----------] 3 tests from CommandLineHelpModuleTest (21 ms total) 7: 7: [----------] 7 tests from CommandLineHelpWriterTest 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (5 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (6 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms) 7: [----------] 7 tests from CommandLineHelpWriterTest (14 ms total) 7: 7: [----------] 6 tests from CommandLineModuleManagerTest 7: [ RUN ] CommandLineModuleManagerTest.RunsModule 7: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 7: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 7: 7: [----------] 13 tests from CommandLineParserTest 7: [ RUN ] CommandLineParserTest.HandlesSingleValues 7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesString 7: [ OK ] CommandLineParserTest.HandlesString (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 7: [----------] 13 tests from CommandLineParserTest (1 ms total) 7: 7: [----------] 6 tests from CommandLineProgramContextTest 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 7: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 7: 7: [----------] 3 tests from OutputNamesTest 7: [ RUN ] OutputNamesTest.CanBeSuffixed 7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 7: [----------] 3 tests from OutputNamesTest (0 ms total) 7: 7: [----------] 21 tests from ParseCommonArgsTest 7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (1 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 7: [----------] 21 tests from ParseCommonArgsTest (2 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 59 tests from 7 test cases ran. (38 ms total) 7: [ PASSED ] 59 tests. 7/30 Test #7: CommandLineUnitTests ............. Passed 1.18 sec test 8 Start 8: DomDecTests 8: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/DomDecTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 9 tests from 2 test cases. 8: [----------] Global test environment set-up. 8: [----------] 7 tests from HashedMap 8: [ RUN ] HashedMap.InsertsFinds 8: [ OK ] HashedMap.InsertsFinds (0 ms) 8: [ RUN ] HashedMap.NegativeKeysWork 8: [ OK ] HashedMap.NegativeKeysWork (0 ms) 8: [ RUN ] HashedMap.InsertsErases 8: [ OK ] HashedMap.InsertsErases (0 ms) 8: [ RUN ] HashedMap.InsertsOrAssigns 8: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 8: [ RUN ] HashedMap.Clears 8: [ OK ] HashedMap.Clears (0 ms) 8: [ RUN ] HashedMap.LinkedEntries 8: [ OK ] HashedMap.LinkedEntries (0 ms) 8: [ RUN ] HashedMap.ResizesTable 8: [ OK ] HashedMap.ResizesTable (0 ms) 8: [----------] 7 tests from HashedMap (0 ms total) 8: 8: [----------] 2 tests from LocalAtomSetManager 8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 8: [----------] 2 tests from LocalAtomSetManager (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 9 tests from 2 test cases ran. (0 ms total) 8: [ PASSED ] 9 tests. 8/30 Test #8: DomDecTests ...................... Passed 1.20 sec test 9 Start 9: EwaldUnitTests 9: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/EwaldUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 257 tests from 10 test cases. 9: [----------] Global test environment set-up. 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (482 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (483 ms total) 9: 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (27 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (6 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (8 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (20 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (8 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (20 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (12 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (24 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (7 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (8 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (13 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (48 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (10 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (8 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (8 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (11 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (12 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (11 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (16 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (8 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (12 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (8 ms) 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (314 ms total) 9: 9: [----------] 144 tests from SaneInput/PmeGatherTest 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (16 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (5 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (12 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (20 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (16 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (3 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (12 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (4 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (5 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (6 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (27 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (6 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (8 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (7 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (0 ms) 9: [----------] 144 tests from SaneInput/PmeGatherTest (648 ms total) 9: 9: [----------] 16 tests from SaneInput/PmeSolveTest 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (7 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (6 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (10 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (7 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (9 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (8 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (7 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (2 ms) 9: [----------] 16 tests from SaneInput/PmeSolveTest (66 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (6 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (5 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (15 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (8 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (8 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (6 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (8 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (7 ms) 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (40 ms total) 9: 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (7 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (10 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (10 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (7 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (9 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (9 ms) 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (68 ms total) 9: 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (10 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (5 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (7 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (8 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (6 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (7 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (66 ms total) 9: 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (6 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (7 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (8 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (8 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (16 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (9 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms) 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (83 ms total) 9: 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (15 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (13 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (24 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (25 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (24 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (15 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (7 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (21 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (16 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (24 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (17 ms) 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (233 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 257 tests from 10 test cases ran. (2187 ms total) 9: [ PASSED ] 257 tests. 9/30 Test #9: EwaldUnitTests ................... Passed 3.60 sec test 10 Start 10: FFTUnitTests 10: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/FFTUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 14 tests from 4 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from ManyFFTTest 10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (72 ms) 10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (141 ms) 10: [----------] 2 tests from ManyFFTTest (214 ms total) 10: 10: [----------] 1 test from FFTTest 10: [ RUN ] FFTTest.Real2DLength18_15Test 10: [ OK ] FFTTest.Real2DLength18_15Test (29 ms) 10: [----------] 1 test from FFTTest (29 ms total) 10: 10: [----------] 1 test from FFFTest3D 10: [ RUN ] FFFTest3D.Real5_6_9 10: [ OK ] FFFTest3D.Real5_6_9 (19 ms) 10: [----------] 1 test from FFFTest3D (19 ms total) 10: 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (5 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (2 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (27 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (14 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (7 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (67 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (113 ms) 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (239 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 14 tests from 4 test cases ran. (501 ms total) 10: [ PASSED ] 14 tests. 10/30 Test #10: FFTUnitTests ..................... Passed 1.82 sec test 11 Start 11: GpuUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/GpuUtilsUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 62 tests from 20 test cases. 11: [----------] Global test environment set-up. 11: [----------] 2 tests from ClfftInitializer 11: [ RUN ] ClfftInitializer.SingleInitializationWorks 11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 11: [ RUN ] ClfftInitializer.TwoInitializationsWork 11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 11: [----------] 2 tests from ClfftInitializer (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Swap 11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Comparison 11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Swap 11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Comparison 11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Swap 11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Comparison 11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Swap 11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Comparison 11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 11: 11: [----------] 1 test from HostAllocatorUntypedTest 11: [ RUN ] HostAllocatorUntypedTest.Comparison 11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/3 (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 62 tests from 20 test cases ran. (1 ms total) 11: [ PASSED ] 62 tests. 11/30 Test #11: GpuUtilsUnitTests ................ Passed 1.14 sec test 12 Start 12: HardwareUnitTests 12: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/HardwareUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 4 tests from 1 test case. 12: [----------] Global test environment set-up. 12: [----------] 4 tests from HardwareTopologyTest 12: [ RUN ] HardwareTopologyTest.Execute 12: [ OK ] HardwareTopologyTest.Execute (98 ms) 12: [ RUN ] HardwareTopologyTest.HwlocExecute 12: [ OK ] HardwareTopologyTest.HwlocExecute (103 ms) 12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (94 ms) 12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (100 ms) 12: [----------] 4 tests from HardwareTopologyTest (411 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 4 tests from 1 test case ran. (411 ms total) 12: [ PASSED ] 4 tests. 12/30 Test #12: HardwareUnitTests ................ Passed 1.60 sec test 13 Start 13: MathUnitTests 13: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/MathUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 204 tests from 29 test cases. 13: [----------] Global test environment set-up. 13: [----------] 1 test from EmptyArrayRefWithPaddingTest 13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 13: 13: [----------] 8 tests from TranslateAndScaleTest 13: [ RUN ] TranslateAndScaleTest.identityTransformation 13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingIdentity 13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (1 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 13: [----------] 8 tests from TranslateAndScaleTest (1 ms total) 13: 13: [----------] 12 tests from DensitySimilarityTest 13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (21 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (81 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (93 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (62 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (25 ms) 13: [----------] 12 tests from DensitySimilarityTest (282 ms total) 13: 13: [----------] 6 tests from StructureSimilarityTest 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 13: [----------] 6 tests from StructureSimilarityTest (0 ms total) 13: 13: [----------] 8 tests from ExponentialMovingAverage 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 13: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 13: 13: [----------] 21 tests from FunctionTest 13: [ RUN ] FunctionTest.StaticLog2 13: [ OK ] FunctionTest.StaticLog2 (7 ms) 13: [ RUN ] FunctionTest.Log2I32Bit 13: [ OK ] FunctionTest.Log2I32Bit (4 ms) 13: [ RUN ] FunctionTest.Log2I64Bit 13: [ OK ] FunctionTest.Log2I64Bit (20 ms) 13: [ RUN ] FunctionTest.GreatestCommonDivisor 13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 13: [ RUN ] FunctionTest.InvsqrtFloat 13: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvsqrtDouble 13: [ OK ] FunctionTest.InvsqrtDouble (7 ms) 13: [ RUN ] FunctionTest.InvsqrtInteger 13: [ OK ] FunctionTest.InvsqrtInteger (1 ms) 13: [ RUN ] FunctionTest.InvcbrtFloat 13: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvcbrtDouble 13: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvcbrtInteger 13: [ OK ] FunctionTest.InvcbrtInteger (7 ms) 13: [ RUN ] FunctionTest.SixthrootFloat 13: [ OK ] FunctionTest.SixthrootFloat (1 ms) 13: [ RUN ] FunctionTest.SixthrootDouble 13: [ OK ] FunctionTest.SixthrootDouble (1 ms) 13: [ RUN ] FunctionTest.SixthrootInteger 13: [ OK ] FunctionTest.SixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootFloat 13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootDouble 13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootInteger 13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.Powers 13: [ OK ] FunctionTest.Powers (0 ms) 13: [ RUN ] FunctionTest.ErfInvFloat 13: [ OK ] FunctionTest.ErfInvFloat (1 ms) 13: [ RUN ] FunctionTest.ErfInvDouble 13: [ OK ] FunctionTest.ErfInvDouble (5 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 13: [----------] 21 tests from FunctionTest (56 ms total) 13: 13: [----------] 4 tests from GaussianOn1DLattice 13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 13: [ RUN ] GaussianOn1DLattice.isCorrect 13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 13: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 13: 13: [----------] 9 tests from GaussTransformTest 13: [ RUN ] GaussTransformTest.isZeroUponConstruction 13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 13: [ RUN ] GaussTransformTest.view 13: [ OK ] GaussTransformTest.view (0 ms) 13: [----------] 9 tests from GaussTransformTest (0 ms total) 13: 13: [----------] 3 tests from DensityFittingForce 13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 13: [ RUN ] DensityFittingForce.pullsTowardsDerivative 13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 13: [----------] 3 tests from DensityFittingForce (0 ms total) 13: 13: [----------] 2 tests from InvertMatrixTest 13: [ RUN ] InvertMatrixTest.IdentityIsImpotent 13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertMatrixTest.ComputesInverse 13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 13: [----------] 2 tests from InvertMatrixTest (0 ms total) 13: 13: [----------] 2 tests from InvertBoxMatrixTest 13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 13: 13: [----------] 15 tests from MatrixTest 13: [ RUN ] MatrixTest.canSetFromArray 13: [ OK ] MatrixTest.canSetFromArray (0 ms) 13: [ RUN ] MatrixTest.canSetStaticallyFromList 13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 13: [ RUN ] MatrixTest.canConstructAndFill 13: [ OK ] MatrixTest.canConstructAndFill (0 ms) 13: [ RUN ] MatrixTest.canSetValues 13: [ OK ] MatrixTest.canSetValues (0 ms) 13: [ RUN ] MatrixTest.canCopyAssign 13: [ OK ] MatrixTest.canCopyAssign (0 ms) 13: [ RUN ] MatrixTest.canSwap 13: [ OK ] MatrixTest.canSwap (0 ms) 13: [ RUN ] MatrixTest.staticMultiDimArrayExtent 13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MatrixTest.determinantWorks 13: [ OK ] MatrixTest.determinantWorks (0 ms) 13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 13: [ RUN ] MatrixTest.traceWorks 13: [ OK ] MatrixTest.traceWorks (0 ms) 13: [ RUN ] MatrixTest.transposeWorks 13: [ OK ] MatrixTest.transposeWorks (0 ms) 13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 13: [ RUN ] MatrixTest.canFillLegacyMatrix 13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 13: [----------] 15 tests from MatrixTest (0 ms total) 13: 13: [----------] 25 tests from MultiDimArrayTest 13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapStatic 13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapDynamic 13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToView 13: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToConstView 13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 13: [ RUN ] MultiDimArrayTest.viewBegin 13: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.viewEnd 13: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstBegin 13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstEnd 13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 13: [----------] 25 tests from MultiDimArrayTest (1 ms total) 13: 13: [----------] 4 tests from MultiDimArrayToMdSpanTest 13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanCopyAssign 13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanMoveAssign 13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanSwap 13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanCopyAssign 13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanMoveAssign 13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanSwap 13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanCopyAssign 13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanMoveAssign 13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanSwap 13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanCopyAssign 13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanMoveAssign 13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanSwap 13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanCopyAssign 13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanMoveAssign 13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanSwap 13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanCopyAssign 13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanMoveAssign 13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanSwap 13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanCopyAssign 13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanMoveAssign 13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanSwap 13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanCopyAssign 13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanMoveAssign 13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanSwap 13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanCopyAssign 13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanMoveAssign 13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanSwap 13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanCopyAssign 13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanMoveAssign 13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanSwap 13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 13: 13: [----------] 37 tests from RVecTest 13: [ RUN ] RVecTest.CanBeStoredInVector 13: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAsMutable_rvec 13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Array 13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 13: [ RUN ] RVecTest.CanAddRVecToRvec 13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanAddAssignRVecToRvec 13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractRVecFromRvec 13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanDotProductRVecByRvec 13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanCrossProductRVecByRvec 13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVecInplace 13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 13: [ RUN ] RVecTest.CanScaleRVec 13: [ OK ] RVecTest.CanScaleRVec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVec 13: [ OK ] RVecTest.CanDivideRVec (0 ms) 13: [ RUN ] RVecTest.CanDoUnitvFromRVec 13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanSqLengthOfRVec 13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanLengthOfRVec 13: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToRVec 13: [ OK ] RVecTest.CanCastToRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToDVec 13: [ OK ] RVecTest.CanCastToDVec (0 ms) 13: [ RUN ] RVecTest.CanLeftScalarMultiply 13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanRightScalarMultiply 13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanGetUnitvFromRVec 13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanGetSqLengthOfRVec 13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanGetLengthOfRVec 13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoCrossProductOfRVec 13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoDotProductOfRVec 13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanScaleByVector 13: [ OK ] RVecTest.CanScaleByVector (0 ms) 13: [ RUN ] RVecTest.asIVec 13: [ OK ] RVecTest.asIVec (0 ms) 13: [ RUN ] RVecTest.elementWiseMin 13: [ OK ] RVecTest.elementWiseMin (0 ms) 13: [ RUN ] RVecTest.elementWiseMax 13: [ OK ] RVecTest.elementWiseMax (0 ms) 13: [ RUN ] RVecTest.WorksAs_dvec_Reference 13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_ivec_Reference 13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Reference 13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 13: [ RUN ] RVecTest.CopyConstructorWorks 13: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 13: [ RUN ] RVecTest.CopyAssignmentWorks 13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] RVecTest.MoveConstructorWorks 13: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 13: [ RUN ] RVecTest.MoveAssignmentWorks 13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 13: [----------] 37 tests from RVecTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 204 tests from 29 test cases ran. (341 ms total) 13: [ PASSED ] 204 tests. 13/30 Test #13: MathUnitTests .................... Passed 1.52 sec test 14 Start 14: MdrunUtilityUnitTests 14: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 17 tests from 1 test case. 14: [----------] Global test environment set-up. 14: [----------] 17 tests from ThreadAffinityTest 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 14: NOTE: Affinity setting failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (18 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 14: NOTE: Affinity setting for 1/2 threads failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 14: [----------] 17 tests from ThreadAffinityTest (21 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 17 tests from 1 test case ran. (21 ms total) 14: [ PASSED ] 17 tests. 14/30 Test #14: MdrunUtilityUnitTests ............ Passed 1.19 sec test 15 Start 15: MdrunUtilityMpiUnitTests 15: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "-host" "localhost" "/build/reproducible-path/gromacs-2020.6/build/openmpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 13 tests from 2 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from ThreadAffinityMultiRankTest 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (44 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (20 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (13 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (17 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (1 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (6 ms) 15: [----------] 6 tests from ThreadAffinityMultiRankTest (121 ms total) 15: 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (4 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (8 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (0 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (0 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (13 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (1 ms) 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (52 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 13 tests from 2 test cases ran. (173 ms total) 15: [ PASSED ] 13 tests. 15/30 Test #15: MdrunUtilityMpiUnitTests ......... Passed 1.60 sec test 16 Start 16: MDSpanTests 16: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/MDSpanTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 32 tests from 7 test cases. 16: [----------] Global test environment set-up. 16: [----------] 4 tests from BasicAccessorPolicy 16: [ RUN ] BasicAccessorPolicy.Decay 16: [ OK ] BasicAccessorPolicy.Decay (0 ms) 16: [ RUN ] BasicAccessorPolicy.Access 16: [ OK ] BasicAccessorPolicy.Access (0 ms) 16: [ RUN ] BasicAccessorPolicy.Offset 16: [ OK ] BasicAccessorPolicy.Offset (0 ms) 16: [ RUN ] BasicAccessorPolicy.CopyAccessor 16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 16: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 16: 16: [----------] 4 tests from ExtentsTest 16: [ RUN ] ExtentsTest.Construction 16: [ OK ] ExtentsTest.Construction (0 ms) 16: [ RUN ] ExtentsTest.PurelyStatic 16: [ OK ] ExtentsTest.PurelyStatic (0 ms) 16: [ RUN ] ExtentsTest.RankNought 16: [ OK ] ExtentsTest.RankNought (0 ms) 16: [ RUN ] ExtentsTest.Assignment 16: [ OK ] ExtentsTest.Assignment (0 ms) 16: [----------] 4 tests from ExtentsTest (0 ms total) 16: 16: [----------] 8 tests from MdSpanExtension 16: [ RUN ] MdSpanExtension.SlicingAllStatic 16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingDynamic 16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingAllStatic3D 16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 16: [ RUN ] MdSpanExtension.SlicingEqualsView3D 16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 16: [ RUN ] MdSpanExtension.additionWorks 16: [ OK ] MdSpanExtension.additionWorks (0 ms) 16: [ RUN ] MdSpanExtension.subtractionWorks 16: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 16: [ RUN ] MdSpanExtension.multiplicationWorks 16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 16: [ RUN ] MdSpanExtension.divisionWorks 16: [ OK ] MdSpanExtension.divisionWorks (0 ms) 16: [----------] 8 tests from MdSpanExtension (0 ms total) 16: 16: [----------] 3 tests from LayoutTests 16: [ RUN ] LayoutTests.LayoutRightConstruction 16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 16: [ RUN ] LayoutTests.LayoutRightProperties 16: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 16: [ RUN ] LayoutTests.LayoutRightOperator 16: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 16: [----------] 3 tests from LayoutTests (0 ms total) 16: 16: [----------] 1 test from MdSpanTest 16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 16: [----------] 1 test from MdSpanTest (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/0.Rank 16: [ OK ] MdSpanTest/0.Rank (0 ms) 16: [ RUN ] MdSpanTest/0.DynamicRank 16: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/0.Extents 16: [ OK ] MdSpanTest/0.Extents (0 ms) 16: [ RUN ] MdSpanTest/0.Strides 16: [ OK ] MdSpanTest/0.Strides (0 ms) 16: [ RUN ] MdSpanTest/0.Properties 16: [ OK ] MdSpanTest/0.Properties (0 ms) 16: [ RUN ] MdSpanTest/0.Operator 16: [ OK ] MdSpanTest/0.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/0 (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/1.Rank 16: [ OK ] MdSpanTest/1.Rank (0 ms) 16: [ RUN ] MdSpanTest/1.DynamicRank 16: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/1.Extents 16: [ OK ] MdSpanTest/1.Extents (0 ms) 16: [ RUN ] MdSpanTest/1.Strides 16: [ OK ] MdSpanTest/1.Strides (0 ms) 16: [ RUN ] MdSpanTest/1.Properties 16: [ OK ] MdSpanTest/1.Properties (0 ms) 16: [ RUN ] MdSpanTest/1.Operator 16: [ OK ] MdSpanTest/1.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/1 (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 32 tests from 7 test cases ran. (0 ms total) 16: [ PASSED ] 32 tests. 16/30 Test #16: MDSpanTests ...................... Passed 1.29 sec test 17 Start 17: OnlineHelpUnitTests 17: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/OnlineHelpUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 22 tests from 4 test cases. 17: [----------] Global test environment set-up. 17: [----------] 6 tests from TextTableFormatterTest 17: [ RUN ] TextTableFormatterTest.HandlesBasicCase 17: [ OK ] TextTableFormatterTest.HandlesBasicCase (3 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (4 ms) 17: [ RUN ] TextTableFormatterTest.HandlesIndentation 17: [ OK ] TextTableFormatterTest.HandlesIndentation (4 ms) 17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (4 ms) 17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (3 ms) 17: [----------] 6 tests from TextTableFormatterTest (19 ms total) 17: 17: [----------] 3 tests from HelpManagerTest 17: [ RUN ] HelpManagerTest.HandlesRootTopic 17: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms) 17: [ RUN ] HelpManagerTest.HandlesSubTopics 17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 17: [ RUN ] HelpManagerTest.HandlesInvalidTopics 17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 17: [----------] 3 tests from HelpManagerTest (1 ms total) 17: 17: [----------] 2 tests from HelpTopicFormattingTest 17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (3 ms) 17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms) 17: [----------] 2 tests from HelpTopicFormattingTest (4 ms total) 17: 17: [----------] 11 tests from HelpWriterContextTest 17: [ RUN ] HelpWriterContextTest.FormatsParagraphs 17: [ OK ] HelpWriterContextTest.FormatsParagraphs (3 ms) 17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms) 17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralText 17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsBulletList 17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsGridTable 17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsTitles 17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 17: [----------] 11 tests from HelpWriterContextTest (4 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 22 tests from 4 test cases ran. (28 ms total) 17: [ PASSED ] 22 tests. 17/30 Test #17: OnlineHelpUnitTests .............. Passed 1.45 sec test 18 Start 18: OptionsUnitTests 18: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/OptionsUnitTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 110 tests from 18 test cases. 18: [----------] Global test environment set-up. 18: [----------] 5 tests from AbstractOptionStorageTest 18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 18: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 18: 18: [----------] 8 tests from FileNameOptionTest 18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (1 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 18: [----------] 8 tests from FileNameOptionTest (1 ms total) 18: 18: [----------] 15 tests from FileNameOptionManagerTest 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 18: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 18: 18: [----------] 1 test from OptionsTest 18: [ RUN ] OptionsTest.FailsOnNonsafeStorage 18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 18: [----------] 1 test from OptionsTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerTest 18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMissingValue 18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesExtraValue 18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesGroups 18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesSections 18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 18: [----------] 9 tests from OptionsAssignerTest (0 ms total) 18: 18: [----------] 4 tests from OptionsAssignerBooleanTest 18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 18: 18: [----------] 13 tests from OptionsAssignerIntegerTest 18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (1 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 18: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total) 18: 18: [----------] 5 tests from OptionsAssignerDoubleTest 18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerStringTest 18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 18: 18: [----------] 6 tests from OptionsAssignerEnumTest 18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 18: 18: [----------] 8 tests from RepeatingOptionSectionTest 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 18: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 18: 18: [----------] 1 test from TimeUnitManagerTest 18: [ RUN ] TimeUnitManagerTest.BasicOperations 18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 18: [----------] 1 test from TimeUnitManagerTest (0 ms total) 18: 18: [----------] 4 tests from TimeUnitBehaviorTest 18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 18: 18: [----------] 2 tests from TreeValueSupportAssignTest 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 18: 18: [----------] 1 test from TreeValueSupportAssignErrorTest 18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 18: 18: [----------] 5 tests from TreeValueSupportCheckTest 18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 18: 18: [----------] 6 tests from TreeValueSupportAdjustTest 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (2 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (5 ms) 18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (6 ms) 18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (3 ms) 18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 18: [----------] 6 tests from TreeValueSupportAdjustTest (18 ms total) 18: 18: [----------] 8 tests from TreeValueSupportTest 18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsInt64Option 18: [ OK ] TreeValueSupportTest.SupportsInt64Option (3 ms) 18: [ RUN ] TreeValueSupportTest.SupportsStringOption 18: [ OK ] TreeValueSupportTest.SupportsStringOption (1 ms) 18: [ RUN ] TreeValueSupportTest.SupportsFloatOption 18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumOption 18: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 18: [----------] 8 tests from TreeValueSupportTest (4 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 110 tests from 18 test cases ran. (24 ms total) 18: [ PASSED ] 110 tests. 18/30 Test #18: OptionsUnitTests ................. Passed 1.41 sec test 19 Start 19: PbcutilUnitTest 19: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/PbcutilUnitTest.xml" 19: Test timeout computed to be: 30 19: [==========] Running 3 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 1 test from PbcTest 19: [ RUN ] PbcTest.CalcShiftsWorks 19: [ OK ] PbcTest.CalcShiftsWorks (24 ms) 19: [----------] 1 test from PbcTest (24 ms total) 19: 19: [----------] 2 tests from PbcEnumsTest 19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 19: [----------] 2 tests from PbcEnumsTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 3 tests from 2 test cases ran. (24 ms total) 19: [ PASSED ] 3 tests. 19/30 Test #19: PbcutilUnitTest .................. Passed 1.46 sec test 20 Start 20: RandomUnitTests 20: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/RandomUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 44 tests from 10 test cases. 20: [----------] Global test environment set-up. 20: [----------] 4 tests from ExponentialDistributionTest 20: [ RUN ] ExponentialDistributionTest.Output 20: [ OK ] ExponentialDistributionTest.Output (7 ms) 20: [ RUN ] ExponentialDistributionTest.Logical 20: [ OK ] ExponentialDistributionTest.Logical (0 ms) 20: [ RUN ] ExponentialDistributionTest.Reset 20: [ OK ] ExponentialDistributionTest.Reset (0 ms) 20: [ RUN ] ExponentialDistributionTest.AltParam 20: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from ExponentialDistributionTest (7 ms total) 20: 20: [----------] 4 tests from GammaDistributionTest 20: [ RUN ] GammaDistributionTest.Output 20: [ OK ] GammaDistributionTest.Output (8 ms) 20: [ RUN ] GammaDistributionTest.Logical 20: [ OK ] GammaDistributionTest.Logical (0 ms) 20: [ RUN ] GammaDistributionTest.Reset 20: [ OK ] GammaDistributionTest.Reset (0 ms) 20: [ RUN ] GammaDistributionTest.AltParam 20: [ OK ] GammaDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from GammaDistributionTest (9 ms total) 20: 20: [----------] 4 tests from NormalDistributionTest 20: [ RUN ] NormalDistributionTest.Output 20: [ OK ] NormalDistributionTest.Output (0 ms) 20: [ RUN ] NormalDistributionTest.Logical 20: [ OK ] NormalDistributionTest.Logical (0 ms) 20: [ RUN ] NormalDistributionTest.Reset 20: [ OK ] NormalDistributionTest.Reset (0 ms) 20: [ RUN ] NormalDistributionTest.AltParam 20: [ OK ] NormalDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from NormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from SeedTest 20: [ RUN ] SeedTest.makeRandomSeed 20: [ OK ] SeedTest.makeRandomSeed (0 ms) 20: [----------] 1 test from SeedTest (0 ms total) 20: 20: [----------] 6 tests from TabulatedNormalDistributionTest 20: [ RUN ] TabulatedNormalDistributionTest.Output14 20: [ OK ] TabulatedNormalDistributionTest.Output14 (8 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Output16 20: [ OK ] TabulatedNormalDistributionTest.Output16 (11 ms) 20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (3 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Logical 20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Reset 20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.AltParam 20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 20: [----------] 6 tests from TabulatedNormalDistributionTest (23 ms total) 20: 20: [----------] 1 test from TabulatedNormalDistributionTableTest 20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (2 ms) 20: [----------] 1 test from TabulatedNormalDistributionTableTest (2 ms total) 20: 20: [----------] 6 tests from ThreeFry2x64Test 20: [ RUN ] ThreeFry2x64Test.Logical 20: [ OK ] ThreeFry2x64Test.Logical (0 ms) 20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 20: [ RUN ] ThreeFry2x64Test.Reseed 20: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 20: [ RUN ] ThreeFry2x64Test.Discard 20: [ OK ] ThreeFry2x64Test.Discard (0 ms) 20: [ RUN ] ThreeFry2x64Test.InvalidCounter 20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 20: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 20: 20: [----------] 4 tests from UniformIntDistributionTest 20: [ RUN ] UniformIntDistributionTest.Output 20: [ OK ] UniformIntDistributionTest.Output (6 ms) 20: [ RUN ] UniformIntDistributionTest.Logical 20: [ OK ] UniformIntDistributionTest.Logical (0 ms) 20: [ RUN ] UniformIntDistributionTest.Reset 20: [ OK ] UniformIntDistributionTest.Reset (0 ms) 20: [ RUN ] UniformIntDistributionTest.AltParam 20: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from UniformIntDistributionTest (6 ms total) 20: 20: [----------] 5 tests from UniformRealDistributionTest 20: [ RUN ] UniformRealDistributionTest.GenerateCanonical 20: [ OK ] UniformRealDistributionTest.GenerateCanonical (3 ms) 20: [ RUN ] UniformRealDistributionTest.Output 20: [ OK ] UniformRealDistributionTest.Output (0 ms) 20: [ RUN ] UniformRealDistributionTest.Logical 20: [ OK ] UniformRealDistributionTest.Logical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Reset 20: [ OK ] UniformRealDistributionTest.Reset (0 ms) 20: [ RUN ] UniformRealDistributionTest.AltParam 20: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 20: [----------] 5 tests from UniformRealDistributionTest (4 ms total) 20: 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (3 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (1 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (3 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (8 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 44 tests from 10 test cases ran. (60 ms total) 20: [ PASSED ] 44 tests. 20/30 Test #20: RandomUnitTests .................. Passed 1.47 sec test 21 Start 21: RestraintTests 21: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/RestraintTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 1 test from 1 test case. 21: [----------] Global test environment set-up. 21: [----------] 1 test from RestraintManager 21: [ RUN ] RestraintManager.restraintList 21: [ OK ] RestraintManager.restraintList (0 ms) 21: [----------] 1 test from RestraintManager (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1 test from 1 test case ran. (0 ms total) 21: [ PASSED ] 1 test. 21/30 Test #21: RestraintTests ................... Passed 1.14 sec test 22 Start 22: TableUnitTests 22: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/TableUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 20 tests from 2 test cases. 22: [----------] Global test environment set-up. 22: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 22: [ RUN ] SplineTableTest/0.Sinc 22: [ OK ] SplineTableTest/0.Sinc (1 ms) 22: [ RUN ] SplineTableTest/0.LJ12 22: [ OK ] SplineTableTest/0.LJ12 (50 ms) 22: [ RUN ] SplineTableTest/0.PmeCorrection 22: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/0.TwoFunctions 22: [ OK ] SplineTableTest/0.TwoFunctions (88 ms) 22: [ RUN ] SplineTableTest/0.ThreeFunctions 22: [ OK ] SplineTableTest/0.ThreeFunctions (88 ms) 22: [ RUN ] SplineTableTest/0.Simd 22: [ OK ] SplineTableTest/0.Simd (22 ms) 22: [ RUN ] SplineTableTest/0.SimdTwoFunctions 22: [ OK ] SplineTableTest/0.SimdTwoFunctions (70 ms) 22: [----------] 10 tests from SplineTableTest/0 (322 ms total) 22: 22: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (6 ms) 22: [ RUN ] SplineTableTest/1.Sinc 22: [ OK ] SplineTableTest/1.Sinc (0 ms) 22: [ RUN ] SplineTableTest/1.LJ12 22: [ OK ] SplineTableTest/1.LJ12 (2 ms) 22: [ RUN ] SplineTableTest/1.PmeCorrection 22: [ OK ] SplineTableTest/1.PmeCorrection (10 ms) 22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/1.TwoFunctions 22: [ OK ] SplineTableTest/1.TwoFunctions (12 ms) 22: [ RUN ] SplineTableTest/1.ThreeFunctions 22: [ OK ] SplineTableTest/1.ThreeFunctions (13 ms) 22: [ RUN ] SplineTableTest/1.Simd 22: [ OK ] SplineTableTest/1.Simd (1 ms) 22: [ RUN ] SplineTableTest/1.SimdTwoFunctions 22: [ OK ] SplineTableTest/1.SimdTwoFunctions (12 ms) 22: [----------] 10 tests from SplineTableTest/1 (57 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 20 tests from 2 test cases ran. (379 ms total) 22: [ PASSED ] 20 tests. 22/30 Test #22: TableUnitTests ................... Passed 1.72 sec test 23 Start 23: TaskAssignmentUnitTests 23: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 2 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms) 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 2 test cases ran. (1 ms total) 23: [ PASSED ] 3 tests. 23/30 Test #23: TaskAssignmentUnitTests .......... Passed 1.18 sec test 24 Start 24: TopologyTest 24: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/TopologyTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 11 tests from 3 test cases. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ExclusionBlockTest 24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 24: [ RUN ] ExclusionBlockTest.MergeExclusions 24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 24: [----------] 3 tests from ExclusionBlockTest (0 ms total) 24: 24: [----------] 2 tests from MtopTest 24: [ RUN ] MtopTest.RangeBasedLoop 24: [ OK ] MtopTest.RangeBasedLoop (0 ms) 24: [ RUN ] MtopTest.Operators 24: [ OK ] MtopTest.Operators (0 ms) 24: [----------] 2 tests from MtopTest (0 ms total) 24: 24: [----------] 6 tests from SymtabTest 24: [ RUN ] SymtabTest.EmptyOnOpen 24: [ OK ] SymtabTest.EmptyOnOpen (0 ms) 24: [ RUN ] SymtabTest.AddSingleEntry 24: [ OK ] SymtabTest.AddSingleEntry (0 ms) 24: [ RUN ] SymtabTest.AddTwoDistinctEntries 24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms) 24: [ RUN ] SymtabTest.TryToAddDuplicates 24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms) 24: [ RUN ] SymtabTest.AddLargeNumberOfEntries 24: [ OK ] SymtabTest.AddLargeNumberOfEntries (15 ms) 24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable 24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms) 24: [----------] 6 tests from SymtabTest (16 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 11 tests from 3 test cases ran. (16 ms total) 24: [ PASSED ] 11 tests. 24/30 Test #24: TopologyTest ..................... Passed 1.40 sec test 25 Start 25: PullTest 25: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/PullTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 5 tests from 1 test case. 25: [----------] Global test environment set-up. 25: [----------] 5 tests from PullTest 25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 25: [----------] 5 tests from PullTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 5 tests from 1 test case ran. (0 ms total) 25: [ PASSED ] 5 tests. 25/30 Test #25: PullTest ......................... Passed 1.26 sec test 26 Start 26: AwhTest 26: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/AwhTest.xml" 26: Test timeout computed to be: 30 26: [==========] Running 12 tests from 4 test cases. 26: [----------] Global test environment set-up. 26: [----------] 1 test from BiasTest 26: [ RUN ] BiasTest.DetectsCovering 26: [ OK ] BiasTest.DetectsCovering (0 ms) 26: [----------] 1 test from BiasTest (0 ms total) 26: 26: [----------] 1 test from gridTest 26: [ RUN ] gridTest.neighborhood 26: [ OK ] gridTest.neighborhood (2 ms) 26: [----------] 1 test from gridTest (2 ms total) 26: 26: [----------] 8 tests from WithParameters/BiasTest 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (21 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (9 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (7 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms) 26: [----------] 8 tests from WithParameters/BiasTest (40 ms total) 26: 26: [----------] 2 tests from WithParameters/BiasStateTest 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms) 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 26: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 12 tests from 4 test cases ran. (43 ms total) 26: [ PASSED ] 12 tests. 26/30 Test #26: AwhTest .......................... Passed 1.16 sec test 27 Start 27: SimdUnitTests 27: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/SimdUnitTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 288 tests from 22 test cases. 27: [----------] Global test environment set-up. 27: [----------] 9 tests from SimdBootstrapTest 27: [ RUN ] SimdBootstrapTest.loadStore 27: [ OK ] SimdBootstrapTest.loadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.loadU 27: [ OK ] SimdBootstrapTest.loadU (0 ms) 27: [ RUN ] SimdBootstrapTest.storeU 27: [ OK ] SimdBootstrapTest.storeU (0 ms) 27: [ RUN ] SimdBootstrapTest.loadStoreI 27: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 27: [ RUN ] SimdBootstrapTest.loadUI 27: [ OK ] SimdBootstrapTest.loadUI (0 ms) 27: [ RUN ] SimdBootstrapTest.storeUI 27: [ OK ] SimdBootstrapTest.storeUI (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadStore 27: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadU 27: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4StoreU 27: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 27: [----------] 9 tests from SimdBootstrapTest (0 ms total) 27: 27: [----------] 1 test from SimdTest 27: [ RUN ] SimdTest.GmxAligned 27: [ OK ] SimdTest.GmxAligned (0 ms) 27: [----------] 1 test from SimdTest (0 ms total) 27: 27: [----------] 42 tests from SimdFloatingpointTest 27: [ RUN ] SimdFloatingpointTest.setZero 27: [ OK ] SimdFloatingpointTest.setZero (0 ms) 27: [ RUN ] SimdFloatingpointTest.set 27: [ OK ] SimdFloatingpointTest.set (0 ms) 27: [ RUN ] SimdFloatingpointTest.add 27: [ OK ] SimdFloatingpointTest.add (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskAdd 27: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 27: [ RUN ] SimdFloatingpointTest.sub 27: [ OK ] SimdFloatingpointTest.sub (0 ms) 27: [ RUN ] SimdFloatingpointTest.mul 27: [ OK ] SimdFloatingpointTest.mul (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzMul 27: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 27: [ RUN ] SimdFloatingpointTest.fma 27: [ OK ] SimdFloatingpointTest.fma (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzFma 27: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fms 27: [ OK ] SimdFloatingpointTest.fms (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnma 27: [ OK ] SimdFloatingpointTest.fnma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnms 27: [ OK ] SimdFloatingpointTest.fnms (0 ms) 27: [ RUN ] SimdFloatingpointTest.abs 27: [ OK ] SimdFloatingpointTest.abs (0 ms) 27: [ RUN ] SimdFloatingpointTest.neg 27: [ OK ] SimdFloatingpointTest.neg (0 ms) 27: [ RUN ] SimdFloatingpointTest.and 27: [ OK ] SimdFloatingpointTest.and (0 ms) 27: [ RUN ] SimdFloatingpointTest.or 27: [ OK ] SimdFloatingpointTest.or (0 ms) 27: [ RUN ] SimdFloatingpointTest.xor 27: [ OK ] SimdFloatingpointTest.xor (0 ms) 27: [ RUN ] SimdFloatingpointTest.andNot 27: [ OK ] SimdFloatingpointTest.andNot (0 ms) 27: [ RUN ] SimdFloatingpointTest.max 27: [ OK ] SimdFloatingpointTest.max (0 ms) 27: [ RUN ] SimdFloatingpointTest.min 27: [ OK ] SimdFloatingpointTest.min (0 ms) 27: [ RUN ] SimdFloatingpointTest.round 27: [ OK ] SimdFloatingpointTest.round (0 ms) 27: [ RUN ] SimdFloatingpointTest.roundMode 27: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 27: [ RUN ] SimdFloatingpointTest.trunc 27: [ OK ] SimdFloatingpointTest.trunc (0 ms) 27: [ RUN ] SimdFloatingpointTest.frexp 27: [ OK ] SimdFloatingpointTest.frexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.ldexp 27: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.rsqrt 27: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRsqrt 27: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.rcp 27: [ OK ] SimdFloatingpointTest.rcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRcp 27: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.selectByNotMask 27: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpNe 27: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLe 27: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLt 27: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 27: [ RUN ] SimdFloatingpointTest.testBits 27: [ OK ] SimdFloatingpointTest.testBits (0 ms) 27: [ RUN ] SimdFloatingpointTest.andB 27: [ OK ] SimdFloatingpointTest.andB (0 ms) 27: [ RUN ] SimdFloatingpointTest.orB 27: [ OK ] SimdFloatingpointTest.orB (0 ms) 27: [ RUN ] SimdFloatingpointTest.anyTrueB 27: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 27: [ RUN ] SimdFloatingpointTest.blend 27: [ OK ] SimdFloatingpointTest.blend (0 ms) 27: [ RUN ] SimdFloatingpointTest.reduce 27: [ OK ] SimdFloatingpointTest.reduce (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 27: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 27: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 27: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 27: 27: [----------] 16 tests from SimdFloatingpointUtilTest 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 27: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 27: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 27: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 27: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 27: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 27: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 27: 27: [----------] 3 tests from SimdVectorOperationsTest 27: [ RUN ] SimdVectorOperationsTest.iprod 27: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 27: [ RUN ] SimdVectorOperationsTest.norm2 27: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 27: [ RUN ] SimdVectorOperationsTest.cprod 27: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 27: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 27: 27: [----------] 56 tests from SimdMathTest 27: [ RUN ] SimdMathTest.generateTestPointsFloat 27: [ OK ] SimdMathTest.generateTestPointsFloat (23 ms) 27: [ RUN ] SimdMathTest.copysign 27: [ OK ] SimdMathTest.copysign (0 ms) 27: [ RUN ] SimdMathTest.invsqrt 27: [ OK ] SimdMathTest.invsqrt (0 ms) 27: [ RUN ] SimdMathTest.maskzInvsqrt 27: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPair 27: [ OK ] SimdMathTest.invsqrtPair (1 ms) 27: [ RUN ] SimdMathTest.sqrt 27: [ OK ] SimdMathTest.sqrt (0 ms) 27: [ RUN ] SimdMathTest.sqrtUnsafe 27: [ OK ] SimdMathTest.sqrtUnsafe (1 ms) 27: [ RUN ] SimdMathTest.inv 27: [ OK ] SimdMathTest.inv (10 ms) 27: [ RUN ] SimdMathTest.maskzInv 27: [ OK ] SimdMathTest.maskzInv (0 ms) 27: [ RUN ] SimdMathTest.cbrt 27: [ OK ] SimdMathTest.cbrt (1 ms) 27: [ RUN ] SimdMathTest.invcbrt 27: [ OK ] SimdMathTest.invcbrt (2 ms) 27: [ RUN ] SimdMathTest.log2 27: [ OK ] SimdMathTest.log2 (0 ms) 27: [ RUN ] SimdMathTest.log 27: [ OK ] SimdMathTest.log (5 ms) 27: [ RUN ] SimdMathTest.exp2 27: [ OK ] SimdMathTest.exp2 (2 ms) 27: [ RUN ] SimdMathTest.exp2Unsafe 27: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 27: [ RUN ] SimdMathTest.exp 27: [ OK ] SimdMathTest.exp (11 ms) 27: [ RUN ] SimdMathTest.expUnsafe 27: [ OK ] SimdMathTest.expUnsafe (0 ms) 27: [ RUN ] SimdMathTest.pow 27: [ OK ] SimdMathTest.pow (0 ms) 27: [ RUN ] SimdMathTest.powUnsafe 27: [ OK ] SimdMathTest.powUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erf 27: [ OK ] SimdMathTest.erf (6 ms) 27: [ RUN ] SimdMathTest.erfc 27: [ OK ] SimdMathTest.erfc (2 ms) 27: [ RUN ] SimdMathTest.sin 27: [ OK ] SimdMathTest.sin (1 ms) 27: [ RUN ] SimdMathTest.cos 27: [ OK ] SimdMathTest.cos (5 ms) 27: [ RUN ] SimdMathTest.tan 27: [ OK ] SimdMathTest.tan (1 ms) 27: [ RUN ] SimdMathTest.asin 27: [ OK ] SimdMathTest.asin (1 ms) 27: [ RUN ] SimdMathTest.acos 27: [ OK ] SimdMathTest.acos (9 ms) 27: [ RUN ] SimdMathTest.atan 27: [ OK ] SimdMathTest.atan (1 ms) 27: [ RUN ] SimdMathTest.atan2 27: [ OK ] SimdMathTest.atan2 (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrection 27: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrection 27: [ OK ] SimdMathTest.pmePotentialCorrection (1 ms) 27: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracy 27: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (9 ms) 27: [ RUN ] SimdMathTest.invSingleAccuracy 27: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.cbrtSingleAccuracy 27: [ OK ] SimdMathTest.cbrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 27: [ OK ] SimdMathTest.invcbrtSingleAccuracy (13 ms) 27: [ RUN ] SimdMathTest.log2SingleAccuracy 27: [ OK ] SimdMathTest.log2SingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.logSingleAccuracy 27: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracy 27: [ OK ] SimdMathTest.exp2SingleAccuracy (3 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 27: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (1 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracy 27: [ OK ] SimdMathTest.expSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (9 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracy 27: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erfSingleAccuracy 27: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.erfcSingleAccuracy 27: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.sinSingleAccuracy 27: [ OK ] SimdMathTest.sinSingleAccuracy (9 ms) 27: [ RUN ] SimdMathTest.cosSingleAccuracy 27: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.tanSingleAccuracy 27: [ OK ] SimdMathTest.tanSingleAccuracy (10 ms) 27: [ RUN ] SimdMathTest.asinSingleAccuracy 27: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.acosSingleAccuracy 27: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.atanSingleAccuracy 27: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atan2SingleAccuracy 27: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (9 ms) 27: [----------] 56 tests from SimdMathTest (163 ms total) 27: 27: [----------] 1 test from EmptyArrayRefTest 27: [ RUN ] EmptyArrayRefTest.IsEmpty 27: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 27: [----------] 1 test from EmptyArrayRefTest (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/0.Assignment 27: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/1.Assignment 27: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/0.Basic 27: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/1.Basic 27: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 27: 27: [----------] 23 tests from SimdIntegerTest 27: [ RUN ] SimdIntegerTest.setZero 27: [ OK ] SimdIntegerTest.setZero (0 ms) 27: [ RUN ] SimdIntegerTest.set 27: [ OK ] SimdIntegerTest.set (0 ms) 27: [ RUN ] SimdIntegerTest.add 27: [ OK ] SimdIntegerTest.add (0 ms) 27: [ RUN ] SimdIntegerTest.sub 27: [ OK ] SimdIntegerTest.sub (0 ms) 27: [ RUN ] SimdIntegerTest.mul 27: [ OK ] SimdIntegerTest.mul (0 ms) 27: [ RUN ] SimdIntegerTest.and 27: [ OK ] SimdIntegerTest.and (0 ms) 27: [ RUN ] SimdIntegerTest.andNot 27: [ OK ] SimdIntegerTest.andNot (0 ms) 27: [ RUN ] SimdIntegerTest.or 27: [ OK ] SimdIntegerTest.or (0 ms) 27: [ RUN ] SimdIntegerTest.xor 27: [ OK ] SimdIntegerTest.xor (0 ms) 27: [ RUN ] SimdIntegerTest.extract 27: [ OK ] SimdIntegerTest.extract (0 ms) 27: [ RUN ] SimdIntegerTest.cvtR2I 27: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvttR2I 27: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvtI2R 27: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpLt 27: [ OK ] SimdIntegerTest.cmpLt (0 ms) 27: [ RUN ] SimdIntegerTest.testBits 27: [ OK ] SimdIntegerTest.testBits (0 ms) 27: [ RUN ] SimdIntegerTest.andB 27: [ OK ] SimdIntegerTest.andB (0 ms) 27: [ RUN ] SimdIntegerTest.orB 27: [ OK ] SimdIntegerTest.orB (0 ms) 27: [ RUN ] SimdIntegerTest.anyTrue 27: [ OK ] SimdIntegerTest.anyTrue (0 ms) 27: [ RUN ] SimdIntegerTest.blend 27: [ OK ] SimdIntegerTest.blend (0 ms) 27: [ RUN ] SimdIntegerTest.cvtB2IB 27: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 27: [ RUN ] SimdIntegerTest.cvtIB2B 27: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 27: [----------] 23 tests from SimdIntegerTest (0 ms total) 27: 27: [----------] 32 tests from Simd4FloatingpointTest 27: [ RUN ] Simd4FloatingpointTest.setZero 27: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 27: [ RUN ] Simd4FloatingpointTest.set 27: [ OK ] Simd4FloatingpointTest.set (0 ms) 27: [ RUN ] Simd4FloatingpointTest.add 27: [ OK ] Simd4FloatingpointTest.add (0 ms) 27: [ RUN ] Simd4FloatingpointTest.sub 27: [ OK ] Simd4FloatingpointTest.sub (0 ms) 27: [ RUN ] Simd4FloatingpointTest.mul 27: [ OK ] Simd4FloatingpointTest.mul (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fma 27: [ OK ] Simd4FloatingpointTest.fma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fms 27: [ OK ] Simd4FloatingpointTest.fms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnma 27: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnms 27: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.abs 27: [ OK ] Simd4FloatingpointTest.abs (0 ms) 27: [ RUN ] Simd4FloatingpointTest.neg 27: [ OK ] Simd4FloatingpointTest.neg (0 ms) 27: [ RUN ] Simd4FloatingpointTest.and 27: [ OK ] Simd4FloatingpointTest.and (0 ms) 27: [ RUN ] Simd4FloatingpointTest.or 27: [ OK ] Simd4FloatingpointTest.or (0 ms) 27: [ RUN ] Simd4FloatingpointTest.xor 27: [ OK ] Simd4FloatingpointTest.xor (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andNot 27: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 27: [ RUN ] Simd4FloatingpointTest.max 27: [ OK ] Simd4FloatingpointTest.max (0 ms) 27: [ RUN ] Simd4FloatingpointTest.min 27: [ OK ] Simd4FloatingpointTest.min (0 ms) 27: [ RUN ] Simd4FloatingpointTest.round 27: [ OK ] Simd4FloatingpointTest.round (0 ms) 27: [ RUN ] Simd4FloatingpointTest.trunc 27: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 27: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 27: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.selectByNotMask 27: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpNe 27: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLe 27: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLt 27: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andB 27: [ OK ] Simd4FloatingpointTest.andB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.orB 27: [ OK ] Simd4FloatingpointTest.orB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.anyTrue 27: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 27: [ RUN ] Simd4FloatingpointTest.blend 27: [ OK ] Simd4FloatingpointTest.blend (0 ms) 27: [ RUN ] Simd4FloatingpointTest.reduce 27: [ OK ] Simd4FloatingpointTest.reduce (1 ms) 27: [ RUN ] Simd4FloatingpointTest.dotProduct 27: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 27: [ RUN ] Simd4FloatingpointTest.transpose 27: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 27: [----------] 32 tests from Simd4FloatingpointTest (1 ms total) 27: 27: [----------] 1 test from Simd4VectorOperationsTest 27: [ RUN ] Simd4VectorOperationsTest.norm2 27: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 27: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 27: 27: [----------] 2 tests from Simd4MathTest 27: [ RUN ] Simd4MathTest.invsqrt 27: [ OK ] Simd4MathTest.invsqrt (0 ms) 27: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 27: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 27: [----------] 2 tests from Simd4MathTest (0 ms total) 27: 27: [----------] 41 tests from SimdScalarTest 27: [ RUN ] SimdScalarTest.load 27: [ OK ] SimdScalarTest.load (0 ms) 27: [ RUN ] SimdScalarTest.loadU 27: [ OK ] SimdScalarTest.loadU (0 ms) 27: [ RUN ] SimdScalarTest.store 27: [ OK ] SimdScalarTest.store (0 ms) 27: [ RUN ] SimdScalarTest.storeU 27: [ OK ] SimdScalarTest.storeU (0 ms) 27: [ RUN ] SimdScalarTest.setZero 27: [ OK ] SimdScalarTest.setZero (0 ms) 27: [ RUN ] SimdScalarTest.andNot 27: [ OK ] SimdScalarTest.andNot (0 ms) 27: [ RUN ] SimdScalarTest.fma 27: [ OK ] SimdScalarTest.fma (0 ms) 27: [ RUN ] SimdScalarTest.fms 27: [ OK ] SimdScalarTest.fms (0 ms) 27: [ RUN ] SimdScalarTest.fnma 27: [ OK ] SimdScalarTest.fnma (0 ms) 27: [ RUN ] SimdScalarTest.fnms 27: [ OK ] SimdScalarTest.fnms (0 ms) 27: [ RUN ] SimdScalarTest.maskAdd 27: [ OK ] SimdScalarTest.maskAdd (0 ms) 27: [ RUN ] SimdScalarTest.maskzMul 27: [ OK ] SimdScalarTest.maskzMul (0 ms) 27: [ RUN ] SimdScalarTest.maskzFma 27: [ OK ] SimdScalarTest.maskzFma (0 ms) 27: [ RUN ] SimdScalarTest.abs 27: [ OK ] SimdScalarTest.abs (0 ms) 27: [ RUN ] SimdScalarTest.max 27: [ OK ] SimdScalarTest.max (0 ms) 27: [ RUN ] SimdScalarTest.min 27: [ OK ] SimdScalarTest.min (0 ms) 27: [ RUN ] SimdScalarTest.round 27: [ OK ] SimdScalarTest.round (0 ms) 27: [ RUN ] SimdScalarTest.trunc 27: [ OK ] SimdScalarTest.trunc (0 ms) 27: [ RUN ] SimdScalarTest.reduce 27: [ OK ] SimdScalarTest.reduce (0 ms) 27: [ RUN ] SimdScalarTest.testBits 27: [ OK ] SimdScalarTest.testBits (0 ms) 27: [ RUN ] SimdScalarTest.anyTrue 27: [ OK ] SimdScalarTest.anyTrue (0 ms) 27: [ RUN ] SimdScalarTest.selectByMask 27: [ OK ] SimdScalarTest.selectByMask (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMask 27: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 27: [ RUN ] SimdScalarTest.blend 27: [ OK ] SimdScalarTest.blend (0 ms) 27: [ RUN ] SimdScalarTest.cvtR2I 27: [ OK ] SimdScalarTest.cvtR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvttR2I 27: [ OK ] SimdScalarTest.cvttR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvtI2R 27: [ OK ] SimdScalarTest.cvtI2R (0 ms) 27: [ RUN ] SimdScalarTest.cvtF2D 27: [ OK ] SimdScalarTest.cvtF2D (0 ms) 27: [ RUN ] SimdScalarTest.cvtD2D 27: [ OK ] SimdScalarTest.cvtD2D (0 ms) 27: [ RUN ] SimdScalarTest.loadI 27: [ OK ] SimdScalarTest.loadI (0 ms) 27: [ RUN ] SimdScalarTest.loadUI 27: [ OK ] SimdScalarTest.loadUI (0 ms) 27: [ RUN ] SimdScalarTest.storeI 27: [ OK ] SimdScalarTest.storeI (0 ms) 27: [ RUN ] SimdScalarTest.storeUI 27: [ OK ] SimdScalarTest.storeUI (0 ms) 27: [ RUN ] SimdScalarTest.andNotI 27: [ OK ] SimdScalarTest.andNotI (0 ms) 27: [ RUN ] SimdScalarTest.testBitsI 27: [ OK ] SimdScalarTest.testBitsI (0 ms) 27: [ RUN ] SimdScalarTest.selectByMaskI 27: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMaskI 27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 27: [ RUN ] SimdScalarTest.blendI 27: [ OK ] SimdScalarTest.blendI (0 ms) 27: [ RUN ] SimdScalarTest.cvtB2IB 27: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 27: [ RUN ] SimdScalarTest.cvtIB2B 27: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 27: [ RUN ] SimdScalarTest.expandScalarsToTriplets 27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 27: [----------] 41 tests from SimdScalarTest (0 ms total) 27: 27: [----------] 8 tests from SimdScalarUtilTest 27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 27: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 27: 27: [----------] 37 tests from SimdScalarMathTest 27: [ RUN ] SimdScalarMathTest.copysign 27: [ OK ] SimdScalarMathTest.copysign (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPair 27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdScalarMathTest.inv 27: [ OK ] SimdScalarMathTest.inv (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrt 27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdScalarMathTest.log 27: [ OK ] SimdScalarMathTest.log (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2 27: [ OK ] SimdScalarMathTest.exp2 (0 ms) 27: [ RUN ] SimdScalarMathTest.exp 27: [ OK ] SimdScalarMathTest.exp (0 ms) 27: [ RUN ] SimdScalarMathTest.erf 27: [ OK ] SimdScalarMathTest.erf (0 ms) 27: [ RUN ] SimdScalarMathTest.erfc 27: [ OK ] SimdScalarMathTest.erfc (0 ms) 27: [ RUN ] SimdScalarMathTest.sincos 27: [ OK ] SimdScalarMathTest.sincos (0 ms) 27: [ RUN ] SimdScalarMathTest.sin 27: [ OK ] SimdScalarMathTest.sin (0 ms) 27: [ RUN ] SimdScalarMathTest.cos 27: [ OK ] SimdScalarMathTest.cos (0 ms) 27: [ RUN ] SimdScalarMathTest.tan 27: [ OK ] SimdScalarMathTest.tan (0 ms) 27: [ RUN ] SimdScalarMathTest.asin 27: [ OK ] SimdScalarMathTest.asin (0 ms) 27: [ RUN ] SimdScalarMathTest.acos 27: [ OK ] SimdScalarMathTest.acos (0 ms) 27: [ RUN ] SimdScalarMathTest.atan 27: [ OK ] SimdScalarMathTest.atan (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2 27: [ OK ] SimdScalarMathTest.atan2 (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrection 27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.invSingleAccuracy 27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.logSingleAccuracy 27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.expSingleAccuracy 27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 27: [----------] 37 tests from SimdScalarMathTest (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 288 tests from 22 test cases ran. (164 ms total) 27: [ PASSED ] 288 tests. 27/30 Test #27: SimdUnitTests .................... Passed 1.50 sec test 28 Start 28: CompatibilityHelpersTests 28: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/CompatibilityHelpersTests.xml" 28: Test timeout computed to be: 30 28: [==========] Running 170 tests from 12 test cases. 28: [----------] Global test environment set-up. 28: [----------] 45 tests from OptionalTest 28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes 28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructEmpty 28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms) 28: [ RUN ] OptionalTest.CanConstructFromNullopt 28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType 28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral 28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting 28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValue 28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting 28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValue 28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral 28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage 28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral 28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromValue 28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignFromValue 28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanResetContent 28: [ OK ] OptionalTest.CanResetContent (0 ms) 28: [ RUN ] OptionalTest.ProvidesRelationalOperators 28: [ OK ] OptionalTest.ProvidesRelationalOperators (1 ms) 28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators 28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.CanProduceHash 28: [ OK ] OptionalTest.CanProduceHash (0 ms) 28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType 28: alignment_of: 1 28: alignment_of: 2 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 16 28: alignment_of: 1 28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms) 28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType 28: sizeof( nonstd::optional_lite::detail::storage_t ): 1 28: sizeof( optional ): 2 (1) 28: sizeof( optional ): 4 (2) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 32 (16) 28: sizeof( optional ): 2 (1) 28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms) 28: [----------] 45 tests from OptionalTest (1 ms total) 28: 28: [----------] 7 tests from MakeOptionalTest 28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] MakeOptionalTest.CanCopyConstruct 28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanMoveConstruct 28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms) 28: [----------] 7 tests from MakeOptionalTest (0 ms total) 28: 28: [----------] 4 tests from OptionalMemberSwapTest 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms) 28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total) 28: 28: [----------] 4 tests from OptionalImplicitValueTest 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms) 28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total) 28: 28: [----------] 20 tests from OptionalIntValueTest 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool 28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms) 28: [----------] 20 tests from OptionalIntValueTest (0 ms total) 28: 28: [----------] 1 test from NotNullConstruction 28: [ RUN ] NotNullConstruction.Works 28: [ OK ] NotNullConstruction.Works (0 ms) 28: [----------] 1 test from NotNullConstruction (0 ms total) 28: 28: [----------] 1 test from NotNullCasting 28: [ RUN ] NotNullCasting.Works 28: [ OK ] NotNullCasting.Works (0 ms) 28: [----------] 1 test from NotNullCasting (0 ms total) 28: 28: [----------] 1 test from NotNullAssignment 28: [ RUN ] NotNullAssignment.Works 28: [ OK ] NotNullAssignment.Works (0 ms) 28: [----------] 1 test from NotNullAssignment (0 ms total) 28: 28: [----------] 1 test from MakeNotNull 28: [ RUN ] MakeNotNull.Works 28: [ OK ] MakeNotNull.Works (0 ms) 28: [----------] 1 test from MakeNotNull (0 ms total) 28: 28: [----------] 1 test from NotNull 28: [ RUN ] NotNull.WorksInContainers 28: [ OK ] NotNull.WorksInContainers (0 ms) 28: [----------] 1 test from NotNull (0 ms total) 28: 28: [----------] 80 tests from StringViewTest 28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView 28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize 28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromCString 28: [ OK ] StringViewTest.CanConstructFromCString (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.AllowForwardIteration 28: [ OK ] StringViewTest.AllowForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstForwardIteration 28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowReverseIteration 28: [ OK ] StringViewTest.AllowReverseIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstReverseIteration 28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms) 28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize 28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms) 28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty 28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex 28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaAt 28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms) 28: [ RUN ] StringViewTest.CanAccessAllElementsViaData 28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms) 28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr 28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms) 28: [ RUN ] StringViewTest.CanRemovePrefix 28: [ OK ] StringViewTest.CanRemovePrefix (0 ms) 28: [ RUN ] StringViewTest.CanRemoveSuffix 28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms) 28: [ RUN ] StringViewTest.CanSwapWithOtherView 28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms) 28: [ RUN ] StringViewTest.CanCopySubstringWithCopy 28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms) 28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr 28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (1 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms) 28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare 28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare 28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCompareToViews 28: [ OK ] StringViewTest.CanCompareToViews (0 ms) 28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView 28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms) 28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual 28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms) 28: [ RUN ] StringViewTest.CanPrintViewToPutputStream 28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms) 28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms) 28: [----------] 80 tests from StringViewTest (1 ms total) 28: 28: [----------] 5 tests from StringViewExtensionTest 28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString 28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms) 28: [----------] 5 tests from StringViewExtensionTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 170 tests from 12 test cases ran. (2 ms total) 28: [ PASSED ] 170 tests. 28/30 Test #28: CompatibilityHelpersTests ........ Passed 1.24 sec test 29 Start 29: FileIOTests 29: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/FileIOTests.xml" 29: Test timeout computed to be: 30 29: [==========] Running 33 tests from 8 test cases. 29: [----------] Global test environment set-up. 29: [----------] 2 tests from FileMD5Test 29: [ RUN ] FileMD5Test.CanComputeMD5 29: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 29: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 29: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 29: [----------] 2 tests from FileMD5Test (1 ms total) 29: 29: [----------] 3 tests from MrcSerializer 29: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 29: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 29: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 29: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 29: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 29: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (1 ms) 29: [----------] 3 tests from MrcSerializer (1 ms total) 29: 29: [----------] 4 tests from MrcDensityMap 29: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 29: [ OK ] MrcDensityMap.RoundTripIsIdempotent (1 ms) 29: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 29: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 29: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 29: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 29: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 29: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (19 ms) 29: [----------] 4 tests from MrcDensityMap (20 ms total) 29: 29: [----------] 8 tests from MrcDensityMapHeaderTest 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 29: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 29: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 29: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.IsSane 29: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 29: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 29: 29: [----------] 9 tests from ReadTest 29: [ RUN ] ReadTest.get_eint_ReadsInteger 29: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side '0.8' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 29: [ RUN ] ReadTest.get_eint_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 29: [ RUN ] ReadTest.get_eint64_ReadsInteger 29: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side '0.8' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 29: [ RUN ] ReadTest.get_eint64_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 29: [ RUN ] ReadTest.get_ereal_ReadsInteger 29: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_ereal_ReadsFloat 29: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 29: [ RUN ] ReadTest.get_ereal_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not a 29: real value 29: 29: 29: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 29: [----------] 9 tests from ReadTest (0 ms total) 29: 29: [----------] 1 test from FileIOXdrSerializerTest 29: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 29: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms) 29: [----------] 1 test from FileIOXdrSerializerTest (1 ms total) 29: 29: [----------] 2 tests from TngTest 29: [ RUN ] TngTest.CanOpenTngFile 29: TNG library: Cannot open file spc2-traj.tng. /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c: 890 29: TNG library: Cannot open file spc2-traj.tng. /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c: 890 29: [ OK ] TngTest.CanOpenTngFile (0 ms) 29: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 29: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 29: [----------] 2 tests from TngTest (0 ms total) 29: 29: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (10 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 29: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (11 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 33 tests from 8 test cases ran. (34 ms total) 29: [ PASSED ] 33 tests. 29/30 Test #29: FileIOTests ...................... Passed 1.20 sec test 30 Start 30: SelectionUnitTests 30: Test command: /build/reproducible-path/gromacs-2020.6/build/openmpi/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2020.6/build/openmpi/Testing/Temporary/SelectionUnitTests.xml" 30: Test timeout computed to be: 30 30: [==========] Running 192 tests from 11 test cases. 30: [----------] Global test environment set-up. 30: [----------] 1 test from IndexGroupTest 30: [ RUN ] IndexGroupTest.RemovesDuplicates 30: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 30: [----------] 1 test from IndexGroupTest (0 ms total) 30: 30: [----------] 15 tests from IndexBlockTest 30: [ RUN ] IndexBlockTest.CreatesUnknownBlock 30: [ OK ] IndexBlockTest.CreatesUnknownBlock (20 ms) 30: [ RUN ] IndexBlockTest.CreatesAtomBlock 30: [ OK ] IndexBlockTest.CreatesAtomBlock (7 ms) 30: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 30: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (12 ms) 30: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 30: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (8 ms) 30: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 30: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (7 ms) 30: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 30: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (4 ms) 30: [ RUN ] IndexBlockTest.CreatesSingleBlock 30: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 30: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 30: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 30: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 30: [----------] 15 tests from IndexBlockTest (61 ms total) 30: 30: [----------] 11 tests from IndexMapTest 30: [ RUN ] IndexMapTest.InitializesAtomBlock 30: [ OK ] IndexMapTest.InitializesAtomBlock (2 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 30: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 30: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (8 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 30: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 30: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (1 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 30: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 30: [ RUN ] IndexMapTest.InitializesMoleculeBlock 30: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms) 30: [ RUN ] IndexMapTest.MapsSingleBlock 30: [ OK ] IndexMapTest.MapsSingleBlock (6 ms) 30: [ RUN ] IndexMapTest.MapsResidueBlocks 30: [ OK ] IndexMapTest.MapsResidueBlocks (8 ms) 30: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 30: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms) 30: [ RUN ] IndexMapTest.HandlesMultipleRequests 30: [ OK ] IndexMapTest.HandlesMultipleRequests (15 ms) 30: [----------] 11 tests from IndexMapTest (43 ms total) 30: 30: [----------] 3 tests from IndexGroupsAndNamesTest 30: [ RUN ] IndexGroupsAndNamesTest.containsNames 30: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 30: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 30: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 30: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 30: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 30: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 30: 30: [----------] 15 tests from NeighborhoodSearchTest 30: [ RUN ] NeighborhoodSearchTest.SimpleSearch 30: [ OK ] NeighborhoodSearchTest.SimpleSearch (27 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 30: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (23 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchBox 30: [ OK ] NeighborhoodSearchTest.GridSearchBox (6 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 30: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (14 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 30: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (8 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 30: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (2 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 30: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (6 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 30: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 30: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (56 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 30: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 30: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 30: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 30: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 30: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (4 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 30: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 30: [----------] 15 tests from NeighborhoodSearchTest (154 ms total) 30: 30: [----------] 12 tests from PositionCalculationTest 30: [ RUN ] PositionCalculationTest.ComputesAtomPositions 30: [ OK ] PositionCalculationTest.ComputesAtomPositions (3 ms) 30: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 30: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 30: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 30: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (3 ms) 30: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 30: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 30: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (17 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 30: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionMask 30: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 30: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 30: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms) 30: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 30: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (6 ms) 30: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 30: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 30: [----------] 12 tests from PositionCalculationTest (36 ms total) 30: 30: [----------] 29 tests from SelectionCollectionTest 30: [ RUN ] SelectionCollectionTest.HandlesNoSelections 30: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 30: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 30: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 30: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 30: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 30: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 30: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 30: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (4 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 30: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 30: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 30: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 30: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 30: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (13 ms) 30: [----------] 29 tests from SelectionCollectionTest (26 ms total) 30: 30: [----------] 14 tests from SelectionCollectionInteractiveTest 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 30: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (7 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 30: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 30: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (14 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (7 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 30: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (8 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 30: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 30: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (20 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 30: [----------] 14 tests from SelectionCollectionInteractiveTest (61 ms total) 30: 30: [----------] 66 tests from SelectionCollectionDataTest 30: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 30: [ OK ] SelectionCollectionDataTest.HandlesAllNone (7 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 30: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResnr 30: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 30: [ OK ] SelectionCollectionDataTest.HandlesResIndex (6 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 30: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 30: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 30: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (19 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 30: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesChain 30: [ OK ] SelectionCollectionDataTest.HandlesChain (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMass 30: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesCharge 30: [ OK ] SelectionCollectionDataTest.HandlesCharge (6 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 30: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 30: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 30: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBeta 30: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResname 30: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 30: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 30: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (5 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (3 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (72 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (33 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (5 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 30: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (3 ms) 30: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 30: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (4 ms) 30: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 30: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 30: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 30: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 30: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (5 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 30: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 30: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (4 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 30: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (3 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (4 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (4 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 30: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 30: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (3 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 30: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 30: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 30: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 30: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 30: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 30: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 30: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 30: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 30: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (3 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 30: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 30: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 30: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (4 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 30: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (4 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 30: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 30: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (3 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 30: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (13 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 30: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 30: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 30: [----------] 66 tests from SelectionCollectionDataTest (266 ms total) 30: 30: [----------] 17 tests from SelectionOptionTest 30: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 30: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 30: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 30: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (5 ms) 30: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 30: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 30: [ RUN ] SelectionOptionTest.ChecksEmptySelections 30: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms) 30: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 30: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooManySelections 30: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 30: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 30: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms) 30: [ RUN ] SelectionOptionTest.HandlesAdjuster 30: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 30: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 30: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 30: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (5 ms) 30: [----------] 17 tests from SelectionOptionTest (13 ms total) 30: 30: [----------] 9 tests from SelectionFileOptionTest 30: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 30: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 30: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 30: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 30: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 30: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 30: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 30: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 30: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 30: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 30: [----------] 9 tests from SelectionFileOptionTest (2 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 192 tests from 11 test cases ran. (662 ms total) 30: [ PASSED ] 192 tests. 30/30 Test #30: SelectionUnitTests ............... Passed 1.79 sec 100% tests passed, 0 tests failed out of 30 Label Time Summary: GTest = 48.36 sec*proc (30 tests) MpiTest = 4.69 sec*proc (3 tests) UnitTest = 48.36 sec*proc (30 tests) Total Test time (real) = 48.84 sec touch build-openmpi dh_testdir # Build speedy, stripped-down version just for documentation generation. # Derived from admin/build-docs.sh (mkdir -p build/documentation ; cd build/documentation; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2020.6/build/documentation/lib \ cmake /build/reproducible-path/gromacs-2020.6 -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None \ -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DGMX_BUILD_MANUAL=ON \ -DGMX_BUILD_HELP=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2") -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test CFLAGS_PRAGMA -- Performing Test CFLAGS_PRAGMA - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_PRAGMA -- Performing Test CXXFLAGS_PRAGMA - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" CMake Warning at cmake/gmxTestImageMagick.cmake:69 (MESSAGE): Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized Call Stack (most recent call first): CMakeLists.txt:897 (GMX_TEST_IMAGEMAGICK) -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "3.4.3", minimum required is "1.6.1") found components: pygments -- Found LATEX: /usr/bin/latex -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.1") found components: doxygen dot -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2020.6/build/documentation /usr/bin/make -j16 gmx -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 gmx make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/documentation/CMakeFiles 58 /usr/bin/make -f CMakeFiles/Makefile2 src/programs/CMakeFiles/gmx.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' Scanning dependencies of target mdrun_objlib /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target release-version-info make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -fno-inline -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -fno-inline -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp Scanning dependencies of target scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target lmfit_objlib /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= Scanning dependencies of target tng_io_obj make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/parser.cpp cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/scanner.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/documentation/tng/include -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/external/zlib -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c 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-I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/documentation/tng/include -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/external/zlib -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c Scanning dependencies of target linearalgebra Scanning dependencies of target tng_io_zlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/documentation/tng/include -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/external/zlib -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/coder.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/external/zlib -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/external/zlib/adler32.c cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/documentation/tng/include -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/external/zlib -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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src/gromacs/CMakeFiles/thread_mpi.dir/build Scanning dependencies of target vmddlopen make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build Scanning dependencies of target modularsimulator make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src 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-fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c Scanning dependencies of target view_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -fno-inline -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /build/reproducible-path/gromacs-2020.6/src/programs/view/view.cpp [ 0%] Built target vmddlopen cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -Wno-redundant-move -std=c++14 -o 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-I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/documentation/tng/include -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/external/zlib -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -isystem /build/reproducible-path/gromacs-2020.6/src/external/thread_mpi/include -g -O2 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-I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/include -I/build/reproducible-path/gromacs-2020.6/build/documentation/tng/include -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/external/zlib -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -fno-inline -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2020.6/build/documentation/src -I/build/reproducible-path/gromacs-2020.6/src -I/build/reproducible-path/gromacs-2020.6/src/external/tng_io/external/zlib -g -O2 -fdebug-prefix-map=/build/reproducible-path/gromacs-2020.6=. 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 2%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' Scanning dependencies of target sphinx-input-rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 2%] Built target linearalgebra /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/plots/xvgr.png /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/plots/xvgr.png cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2020.6/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/docs/conf-vars.py.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/conf-vars.py -D SPHINX_EXTENSION_PATH=/build/reproducible-path/gromacs-2020.6/docs -D RELENG_PATH= -D IMAGE_CONVERT_STRING=impossible -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=1.6.1 -D CMAKE_MINIMUM_REQUIRED_VERSION=3.9.6 -D REQUIRED_CUDA_VERSION=9.0 -D REQUIRED_OPENCL_MIN_VERSION=1.2 -D REQUIRED_CUDA_COMPUTE_CAPABILITY=3.0 -D REGRESSIONTEST_VERSION=2020.6-Debian-2020.6-2 -D SOURCE_MD5SUM=unknown -D REGRESSIONTEST_MD5SUM_STRING=unknown -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR= -P /build/reproducible-path/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/index.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/index.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/download.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/download.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/conf.py /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/conf.py /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend [ 5%] Built target thread_mpi make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/conf-vars.py cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/links.dat /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/links.dat cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/build-system.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/build-system.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/change-management.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/change-management.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/commitstyle.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/commitstyle.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/documentation-generation.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/documentation-generation.rst [ 5%] Built target vmddlopen [ 7%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend [ 7%] Built target view_objlib cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/contribute.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/contribute.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/doxygen.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/doxygen.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/error-handling.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/error-handling.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/formatting.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/formatting.rst Scanning dependencies of target sphinx-image-conversion make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/gmxtree.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/gmxtree.rst make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-image-conversion-timestamp.txt cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/includestyle.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/includestyle.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/index.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/index.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/jenkins.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/jenkins.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/known-issues.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/known-issues.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/language-features.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/language-features.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/naming.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/naming.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/overview.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/overview.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/physical_validation.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/physical_validation.rst [ 7%] Built target sphinx-image-conversion cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/redmine-states.png /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/redmine-states.png cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/relocatable-binaries.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/relocatable-binaries.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/reportstyle.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/reportstyle.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/style.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/style.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/testutils.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/testutils.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/tools.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/tools.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/dev-manual/code-formatting.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/dev-manual/code-formatting.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/fragments/doxygen-links.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/fragments/doxygen-links.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/how-to/index.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/how-to/index.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/how-to/beginners.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/how-to/beginners.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/how-to/topology.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/how-to/topology.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/how-to/special.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/how-to/special.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/how-to/visualize.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/how-to/visualize.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/install-guide/index.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/install-guide/index.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/index.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/index.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/2020.1.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/2020.1.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/2020.2.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/2020.2.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/2020.3.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/2020.3.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/2020.4.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/2020.4.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/2020.5.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/2020.5.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/2020.6.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/2020.6.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/major/highlights.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/major/highlights.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/major/features.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/major/features.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/major/performance.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/major/performance.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/major/tools.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/release-notes/2020/major/tools.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/release-notes/2020/major/bugs-fixed.rst 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/build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/mdrun-performance.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/user-guide/run-time-errors.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/run-time-errors.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/user-guide/security.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/security.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/user-guide/system-preparation.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/system-preparation.rst cd 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/build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/gmxapi/userguide/install.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/gmxapi/userguide/usage.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/gmxapi/userguide/userguide.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/gmxapi/userguide/userguide.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/gmxapi/userguide-stub/pythonreference.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/gmxapi/userguide//pythonreference.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/index.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/index.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/preface.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/preface.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/introduction.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/introduction.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/definitions.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/definitions.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/topologies.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/topologies/particle-type.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/topologies/parameter-files.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/parameter-files.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/topologies/molecule-definition.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/topologies/constraint-algorithm-section.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/constraint-algorithm-section.rst [ 83%] Built target libgromacs cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/topologies/pdb2gmx-input-files.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/topologies/topology-file-formats.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/topologies/force-field-organization.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/force-field-organization.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/file-formats.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/file-formats.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/run-parameters.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/run-parameters.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/details.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/details.rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/averages.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/averages.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/references.rst /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/references.rst /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/plots/peregrine.png /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/plots/peregrine.png cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/plots/adress.png /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/plots/adress.png cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2020.6/docs/reference-manual/plots/plotje.png /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/plots/plotje.png [ 85%] Built target gmx cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input-rst-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 98%] Built target sphinx-input-rst /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake --color= Scanning dependencies of target sphinx-input make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 98%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake --color= Scanning dependencies of target sphinx-programs make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input && /usr/bin/cmake -E make_directory onlinehelp cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input && /build/reproducible-path/gromacs-2020.6/build/documentation/bin/gmx -quiet help -export rst cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-programs-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/man.dir/DependInfo.cmake --color= Scanning dependencies of target man make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/sphinx-build -q -b man -w sphinx-man.log -d /build/reproducible-path/gromacs-2020.6/build/documentation/docs/_doctrees -t do_man /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2020.6/build/documentation/docs/man WARNING: html_static_path entry '_static' does not exist WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/index.rst:13: WARNING: toctree contains reference to nonexisting document 'reference-manual/algorithms' /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/index.rst:13: WARNING: toctree contains reference to nonexisting document 'reference-manual/functions' /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/index.rst:13: WARNING: toctree contains reference to nonexisting document 'reference-manual/special' /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/index.rst:13: WARNING: toctree contains reference to nonexisting document 'reference-manual/analysis' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [100%] Built target man make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' # Generate HTML /usr/bin/make -j16 webpage -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 webpage make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/documentation/CMakeFiles 71 /usr/bin/make -f CMakeFiles/Makefile2 docs/CMakeFiles/webpage.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs/manual /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs/manual /build/reproducible-path/gromacs-2020.6/build/documentation/docs/manual/CMakeFiles/manual.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build Scanning dependencies of target doxygen-source-timestamp make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/doxygen-source-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/build cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/manual && /usr/bin/cmake -E echo "Cannot build PDF manual, because a working form of ImageMagick convert is not available" make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-image-conversion.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' Cannot build PDF manual, because a working form of ImageMagick convert is not available make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 0%] Built target release-version-info [ 0%] Built target doxygen-source-timestamp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend [ 0%] Built target manual /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend [ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend [ 0%] Built target sphinx-image-conversion [ 0%] Built target scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 2%] Built target tng_io_obj make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_zlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 2%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 2%] Built target tng_io_zlib /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/depend /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 2%] Built target linearalgebra cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/CMakeFiles/doxygen-version.dir/DependInfo.cmake --color= [ 2%] Built target vmddlopen [ 5%] Built target thread_mpi make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake --color= [ 5%] Built target view_objlib [ 7%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend Scanning dependencies of target doxygen-version make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2020.6/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/docs/doxygen/Doxyfile-version.cmakein -D VERSION_OUT=Doxyfile-version -P /build/reproducible-path/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E touch Doxyfile-version [ 19%] Built target sphinx-input-rst /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 19%] Built target doxygen-version /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake --color= [ 19%] Built target sphinx-input Scanning dependencies of target doxygen-xml make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=xml -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.1. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 36 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs /build/reproducible-path/gromacs-2020.6/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 92%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs /build/reproducible-path/gromacs-2020.6/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 94%] Built target gmx /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-programs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 95%] Built target sphinx-programs /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/webpage-sphinx.dir/DependInfo.cmake --color= Scanning dependencies of target webpage-sphinx make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/_static cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/sphinx-build -q -b html -w sphinx-html.log -d /build/reproducible-path/gromacs-2020.6/build/documentation/docs/_doctrees /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2020.6/build/documentation/docs/html WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/index.rst:13: WARNING: toctree contains reference to nonexisting document 'reference-manual/algorithms' /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/index.rst:13: WARNING: toctree contains reference to nonexisting document 'reference-manual/functions' /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/index.rst:13: WARNING: toctree contains reference to nonexisting document 'reference-manual/special' /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/index.rst:13: WARNING: toctree contains reference to nonexisting document 'reference-manual/analysis' The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2020.6/src/gromacs/math/vec.h:642: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/settle.cpp:861: warning: Reached end of file while still inside a (nested) comment. Nesting level 1 (probable line reference: 399) /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:68: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_simd_double.h:1626: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_simd_float.h:1514: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_util_double.h:945: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_util_float.h:987: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:821: warning: end of file while inside a group /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp:1458: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/restraintmdmodule.cpp:50: warning: no matching class member found for gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintForceProvider::RestraintForceProvider()=delete' 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/restraintmdmodule.cpp:154: warning: no matching class member found for gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl()=delete' 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(RestraintMDModuleImpl &&) noexcept=default' /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/densityfittingforceprovider.cpp:94: warning: @copybrief or @copydoc target 'DensityFittingForceProvider(const DensityFittingParameters ¶meters)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:198: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:198: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copybrief or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:455: warning: argument 'flags' from the argument list of pme_gpu_try_finish_task has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu.cpp:311: warning: argument 'flags' from the argument list of pme_gpu_try_finish_task has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_math.h:5052: warning: @copydetails or @copydoc target 'pow(SimdFloat)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/densityfittingforceprovider.cpp:94: warning: @copybrief or @copydoc target 'DensityFittingForceProvider(const DensityFittingParameters ¶meters)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/densityfittingforceprovider.cpp:94: warning: @copybrief or @copydoc target 'DensityFittingForceProvider(const DensityFittingParameters ¶meters)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/densityfittingforceprovider.cpp:94: warning: @copydetails or @copydoc target 'DensityFittingForceProvider(const DensityFittingParameters ¶meters)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copybrief or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copybrief or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copydetails or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/restraintmdmodule.h:89: warning: argument 'restraint' from the argument list of gmx::RestraintMDModule::create has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:198: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:198: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copybrief or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copydetails or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/densityfittingforceprovider.cpp:94: warning: @copybrief or @copydoc target 'DensityFittingForceProvider(const DensityFittingParameters ¶meters)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/densityfittingforceprovider.cpp:94: warning: @copydetails or @copydoc target 'DensityFittingForceProvider(const DensityFittingParameters ¶meters)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/restraintmdmodule.h:89: warning: argument 'restraint' from the argument list of gmx::RestraintMDModule::create has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_math.h:5052: warning: @copydetails or @copydoc target 'pow(SimdFloat)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:455: warning: argument 'flags' from the argument list of pme_gpu_try_finish_task has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu.cpp:311: warning: argument 'flags' from the argument list of pme_gpu_try_finish_task has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/warninp.h:107: warning: @copybrief or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/warninp.h:107: warning: @copydetails or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/warninp.h:107: warning: @copybrief or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/warninp.h:107: warning: @copydetails or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/pairlist.cpp:124: warning: argument 'ci' from the argument list of cjFromCi has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_math.h:5052: warning: @copydetails or @copydoc target 'pow(SimdFloat)' not found cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/doxygen-xml-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 97%] Built target doxygen-xml /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/CMakeFiles/dep-graphs-dot.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/CMakeFiles/doxygen-user.dir/DependInfo.cmake --color= Scanning dependencies of target dep-graphs-dot Scanning dependencies of target doxygen-user make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/python3 /build/reproducible-path/gromacs-2020.6/docs/doxygen/graphbuilder.py -S /build/reproducible-path/gromacs-2020.6 -B /build/reproducible-path/gromacs-2020.6/build/documentation --ignore-cycles /build/reproducible-path/gromacs-2020.6/docs/doxygen/cycle-suppressions.txt -o /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/depgraphs /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.1. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 36 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Scanning source tree... Reading source files... Reading Doxygen XML files... Writing graphs... cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/dep-graphs-dot-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 98%] Built target dep-graphs-dot /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/CMakeFiles/doxygen-lib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/CMakeFiles/doxygen-full.dir/DependInfo.cmake --color= Scanning dependencies of target doxygen-lib Scanning dependencies of target doxygen-full make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/depgraphs make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=full -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.1. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... NOTE: You are using Doxygen version 1.9.1. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 36 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 36 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/how-to/special.rst:84: WARNING: undefined label: ff /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/definitions.rst:284: WARNING: undefined label: virial /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/details.rst:241: WARNING: undefined label: lj /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/details.rst:241: WARNING: undefined label: coul /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/details.rst:255: WARNING: undefined label: lj /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/details.rst:257: WARNING: undefined label: coul /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/introduction.rst:306: WARNING: undefined label: em /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies.rst:4: WARNING: undefined label: ff /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:79: WARNING: undefined label: fecalc /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:100: WARNING: undefined label: fecalc /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:100: WARNING: undefined label: dgimplement /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:134: WARNING: undefined label: groupconcept /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst:63: WARNING: undefined label: virtualsites /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst:68: WARNING: undefined label: virtualsites /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst:56: WARNING: undefined label: defaultgroups /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst:151: WARNING: undefined label: charmmff /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:554: WARNING: undefined label: positionrestraint /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:558: WARNING: undefined label: dihedralrestraint /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:565: WARNING: equation not found: eqndphi /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:565: WARNING: equation not found: eqndihre /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:568: WARNING: equation not found: eqndihre /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:571: WARNING: equation not found: eqndihre /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:579: WARNING: undefined label: groupconcept /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:579: WARNING: undefined label: usinggroups /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:718: WARNING: undefined label: positionrestraint /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:726: WARNING: undefined label: fecalc /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:726: WARNING: undefined label: feia /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:867: WARNING: undefined label: pull /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/mdp-options.rst:1139: WARNING: undefined label: reference-manual-position-restraints /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/mdp-options.rst:1151: WARNING: undefined label: reference-manual-position-restraints /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/mdp-options.rst:2983: WARNING: undefined label: electric fields /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/terminology.rst:72: WARNING: undefined label: pbc /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/terminology.rst:135: WARNING: undefined label: temp-coupling /build/reproducible-path/gromacs-2020.6/build/documentation/docs/sphinx-input/user-guide/terminology.rst:370: WARNING: undefined label: md make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 98%] Built target webpage-sphinx libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2020.6/src/gromacs/math/vec.h:642: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/settle.cpp:861: warning: Reached end of file while still inside a (nested) comment. Nesting level 1 (probable line reference: 399) /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:68: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/helpwritercontext.cpp:259: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/testutils/testasserts.cpp:183: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/testutils/testasserts.h:710: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/int64_to_int.h:58: warning: Member int64_to_int found in multiple @ingroup groups! The member will be put in group module_utility, and not in group group_libraryapi /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/basedefinitions.h:213: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.h:109: warning: no matching file member found for void gmx::test::checkEnergiesAgainstReferenceData(const std::string &energyFilename, const std::unordered_map &energyTermsToCompare, gmx::test::TestReferenceChecker *checker) Possible candidates: 'void checkEnergiesAgainstReferenceData(const std::string &energyFilename, const EnergyTermsToCompare &energyTermsToCompare, TestReferenceChecker *checker)' at line 116 of file /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.cpp /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/basedefinitions.h:178: warning: Member INTEL_DIAGNOSTIC_IGNORE(id) (macro definition) of file basedefinitions.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/basedefinitions.h:179: warning: Member INTEL_DIAGNOSTIC_RESET (macro definition) of file basedefinitions.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:200: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:201: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:202: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:203: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:204: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:205: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:206: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:207: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility.h:78: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/int64_to_int.h:49: warning: Found unknown command '\file' /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClCommandQueue (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClProgram (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:134: warning: Member ClKernel (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/vec.h:635: warning: Member norm2(T *v) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:346: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:348: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:349: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:351: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:352: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:354: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:355: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:357: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:358: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/doxygen-user-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 98%] Built target doxygen-user libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2020.6/src/gromacs/math/vec.h:642: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/settle.cpp:861: warning: Reached end of file while still inside a (nested) comment. Nesting level 1 (probable line reference: 399) /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:68: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/onlinehelp/helpwritercontext.cpp:259: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_simd_double.h:1626: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_simd_float.h:1514: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_util_double.h:945: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_util_float.h:987: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:821: warning: end of file while inside a group /build/reproducible-path/gromacs-2020.6/src/testutils/testasserts.cpp:183: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/basedefinitions.h:213: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.h:109: warning: no matching file member found for void gmx::test::checkEnergiesAgainstReferenceData(const std::string &energyFilename, const std::unordered_map &energyTermsToCompare, gmx::test::TestReferenceChecker *checker) Possible candidates: 'void checkEnergiesAgainstReferenceData(const std::string &energyFilename, const EnergyTermsToCompare &energyTermsToCompare, TestReferenceChecker *checker)' at line 116 of file /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.cpp /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:63: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:179: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:185: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:191: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:197: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:203: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:171: warning: Member GMX_PME_SOLVE (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:172: warning: Member GMX_PME_CALC_F (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:173: warning: Member GMX_PME_CALC_ENER_VIR (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:175: warning: Member GMX_PME_CALC_POT (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:177: warning: Member GMX_PME_DO_ALL_F (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:455: warning: argument 'flags' from the argument list of pme_gpu_try_finish_task has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/gmxopencl.h:57: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClCommandQueue (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClProgram (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:134: warning: Member ClKernel (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:646: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:657: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:692: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:703: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:737: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:746: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:656: warning: Member Simd4NFloat (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:702: warning: Member Simd4NDouble (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:745: warning: Member Simd4NReal (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:518: warning: Member load(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:524: warning: Member load(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:542: warning: Member loadU(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:548: warning: Member loadU(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:627: warning: Member load(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:632: warning: Member loadU(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:661: warning: Member loadUNDuplicate4(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:665: warning: Member load4DuplicateN(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:669: warning: Member loadU4NOffset(const float *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:707: warning: Member loadUNDuplicate4(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:711: warning: Member load4DuplicateN(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:715: warning: Member loadU4NOffset(const double *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:380: warning: Member c_simdBestPairAlignment (variable) of gmx is not documented. warning: Included by graph for 'arrayref.h' not generated, too many nodes (52), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (75), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/basedefinitions.h:178: warning: Member INTEL_DIAGNOSTIC_IGNORE(id) (macro definition) of file basedefinitions.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/basedefinitions.h:179: warning: Member INTEL_DIAGNOSTIC_RESET (macro definition) of file basedefinitions.h is not documented. warning: Included by graph for 'classhelpers.h' not generated, too many nodes (90), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:200: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:201: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:202: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:203: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:204: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:205: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:206: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:207: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. warning: Included by graph for 'real.h' not generated, too many nodes (68), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:192: warning: Member toString(bool t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:196: warning: Member toString(int t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:200: warning: Member toString(int64_t t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:204: warning: Member toString(float t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:208: warning: Member toString(double t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:212: warning: Member toString(std::string t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:380: warning: Member c_simdBestPairAlignment (variable) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:656: warning: Member Simd4NFloat (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:702: warning: Member Simd4NDouble (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:745: warning: Member Simd4NReal (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:518: warning: Member load(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:524: warning: Member load(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:542: warning: Member loadU(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:548: warning: Member loadU(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:627: warning: Member load(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:632: warning: Member loadU(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:661: warning: Member loadUNDuplicate4(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:665: warning: Member load4DuplicateN(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:669: warning: Member loadU4NOffset(const float *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:707: warning: Member loadUNDuplicate4(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:711: warning: Member load4DuplicateN(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:715: warning: Member loadU4NOffset(const double *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:646: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:657: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:692: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:703: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:737: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:746: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:452: warning: Member type (typedef) of struct gmx::internal::SimdTraits< SimdFloat > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:454: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< SimdFloat > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:461: warning: Member type (typedef) of struct gmx::internal::SimdTraits< SimdDouble > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:463: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< SimdDouble > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:470: warning: Member type (typedef) of struct gmx::internal::SimdTraits< SimdFInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:472: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< SimdFInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:479: warning: Member type (typedef) of struct gmx::internal::SimdTraits< SimdDInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:481: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< SimdDInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:488: warning: Member type (typedef) of struct gmx::internal::SimdTraits< const T > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:490: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< const T > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:612: warning: Member type (typedef) of struct gmx::internal::Simd4Traits< Simd4Float > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:620: warning: Member type (typedef) of struct gmx::internal::Simd4Traits< Simd4Double > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:453: warning: Member width (variable) of struct gmx::internal::SimdTraits< SimdFloat > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:462: warning: Member width (variable) of struct gmx::internal::SimdTraits< SimdDouble > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:471: warning: Member width (variable) of struct gmx::internal::SimdTraits< SimdFInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:480: warning: Member width (variable) of struct gmx::internal::SimdTraits< SimdDInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:489: warning: Member width (variable) of struct gmx::internal::SimdTraits< const T > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_math.h:5052: warning: @copydetails or @copydoc target 'pow(SimdFloat)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility.h:103: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:192: warning: Member toString(bool t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:196: warning: Member toString(int t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:200: warning: Member toString(int64_t t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:204: warning: Member toString(float t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:208: warning: Member toString(double t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:212: warning: Member toString(std::string t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:65: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:66: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:67: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:68: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:72: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClCommandQueue (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClProgram (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:134: warning: Member ClKernel (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/vec.h:635: warning: Member norm2(T *v) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:192: warning: Member toString(bool t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:196: warning: Member toString(int t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:200: warning: Member toString(int64_t t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:204: warning: Member toString(float t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:208: warning: Member toString(double t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:212: warning: Member toString(std::string t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:380: warning: Member c_simdBestPairAlignment (variable) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:656: warning: Member Simd4NFloat (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:702: warning: Member Simd4NDouble (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:745: warning: Member Simd4NReal (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:518: warning: Member load(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:524: warning: Member load(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:542: warning: Member loadU(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:548: warning: Member loadU(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:627: warning: Member load(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:632: warning: Member loadU(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:661: warning: Member loadUNDuplicate4(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:665: warning: Member load4DuplicateN(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:669: warning: Member loadU4NOffset(const float *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:707: warning: Member loadUNDuplicate4(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:711: warning: Member load4DuplicateN(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:715: warning: Member loadU4NOffset(const double *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:346: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:348: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:349: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:351: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:352: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:354: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:355: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:357: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:358: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:140: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:143: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:145: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:148: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:149: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:150: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:151: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:152: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:153: warning: Member gpuIdsAvailable (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:154: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:157: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:159: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/runner.h:148: warning: Member operator=(Mdrunner &&handle) noexcept(BUGFREE_NOEXCEPT_STRING) (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/runner.h:376: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/manager.h:90: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/manager.h:91: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/manager.h:92: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/restraintmdmodule.h:89: warning: argument 'restraint' from the argument list of gmx::RestraintMDModule::create has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:117: warning: Member iterator_category (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:118: warning: Member value_type (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:119: warning: Member difference_type (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:120: warning: Member pointer (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:121: warning: Member reference (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:158: warning: Member operator!=(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:162: warning: Member operator<(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:166: warning: Member operator>(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:170: warning: Member operator<=(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:174: warning: Member operator>=(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:210: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:274: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:275: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:276: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:298: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:253: warning: Member operator[](const std::size_t index) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:259: warning: Member operator[](const EnumType index) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:264: warning: Member operator[](const EnumType index) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:282: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:283: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:284: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:290: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:291: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:292: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:78: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:79: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:80: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:81: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:82: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:83: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:84: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:85: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:86: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:87: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:88: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:89: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:90: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:104: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:111: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:118: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:125: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:132: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:139: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:146: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:153: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:160: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:167: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:174: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:179: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:185: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:191: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:197: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:203: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:117: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:118: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:129: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:130: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/doxygen-lib-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [ 98%] Built target doxygen-lib The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2020.6/src/gromacs/math/vec.h:642: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/settle.cpp:861: warning: Reached end of file while still inside a (nested) comment. Nesting level 1 (probable line reference: 399) /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:68: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_simd_double.h:1626: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_simd_float.h:1514: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_util_double.h:945: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/impl_reference/impl_reference_util_float.h:987: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:821: warning: end of file while inside a group /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp:1458: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.h:109: warning: no matching file member found for void gmx::test::checkEnergiesAgainstReferenceData(const std::string &energyFilename, const std::unordered_map &energyTermsToCompare, gmx::test::TestReferenceChecker *checker) Possible candidates: 'void checkEnergiesAgainstReferenceData(const std::string &energyFilename, const EnergyTermsToCompare &energyTermsToCompare, TestReferenceChecker *checker)' at line 116 of file /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.cpp /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase.h:117: warning: no matching file member found for std::string gmx::test::prepareMdpFileContents(const std::map &mdpFieldValues) Possible candidates: 'std::string prepareMdpFileContents(const MdpFieldValues &mdpFieldValues)' at line 231 of file /build/reproducible-path/gromacs-2020.6/src/testutils/simulationdatabase.cpp /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:198: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:198: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copybrief or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found warning: Included by graph for 'gmxpre.h' not generated, too many nodes (539), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:63: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:179: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:185: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:191: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:197: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:203: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:171: warning: Member GMX_PME_SOLVE (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:172: warning: Member GMX_PME_CALC_F (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:173: warning: Member GMX_PME_CALC_ENER_VIR (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:175: warning: Member GMX_PME_CALC_POT (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:177: warning: Member GMX_PME_DO_ALL_F (macro definition) of file pme.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme.h:455: warning: argument 'flags' from the argument list of pme_gpu_try_finish_task has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu.cpp:311: warning: argument 'flags' from the argument list of pme_gpu_try_finish_task has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_internal.h:76: warning: Member PME_GRID_C6A (macro definition) of file pme_internal.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_internal.h:82: warning: Member DO_Q_AND_LJ (macro definition) of file pme_internal.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_internal.h:83: warning: Member DO_Q_AND_LJ_LB (macro definition) of file pme_internal.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:75: warning: Member PP_PME_CHARGEB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:76: warning: Member PP_PME_SQRTC6 (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:77: warning: Member PP_PME_SQRTC6B (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:78: warning: Member PP_PME_SIGMA (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:79: warning: Member PP_PME_SIGMAB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:80: warning: Member PP_PME_COORD (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:81: warning: Member PP_PME_ENER_VIR (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:82: warning: Member PP_PME_FINISH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:83: warning: Member PP_PME_SWITCHGRID (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:84: warning: Member PP_PME_RESETCOUNTERS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:85: warning: Member PP_PME_GPUCOMMS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp:72: warning: Member c_int32Value (variable) of gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp:73: warning: Member c_int64Value (variable) of gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp:75: warning: Member c_intAndFloat32 (variable) of gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp:76: warning: Member c_intAndFloat64 (variable) of gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/clfftinitializer.cpp:70: warning: Member g_clfftMutex (variable) of gmx::anonymous_namespace{clfftinitializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/gmxopencl.h:57: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClCommandQueue (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClProgram (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:134: warning: Member ClKernel (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/energyoutput.cpp:91: warning: Member boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/energyoutput.cpp:93: warning: Member tricl_boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/energyoutput.cpp:96: warning: Member vol_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/energyoutput.cpp:98: warning: Member dens_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/energyoutput.cpp:100: warning: Member pv_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/energyoutput.cpp:102: warning: Member enthalpy_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/energyoutput.cpp:104: warning: Member boxvel_nm (variable) of file energyoutput.cpp is not documented. warning: Include graph for 'md.cpp' not generated, too many nodes (56), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp:169: warning: Member minimizersToTest_g (variable) of gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp:171: warning: Member constrainedSystemsToTest_g (variable) of gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp:173: warning: Member minimizersToTestWithConstraints_g (variable) of gmx::test::anonymous_namespace{minimize.cpp} is not documented. warning: Include graph for 'runner.cpp' not generated, too many nodes (79), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp:98: warning: Member c_clSize (variable) of Nbnxm is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_consts.h:46: warning: Member GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_DEFAULT (macro definition) of file nbnxm_ocl_consts.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_consts.h:48: warning: Member GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY (macro definition) of file nbnxm_ocl_consts.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_data_mgmt.cpp:89: warning: Member CL_CONTEXT_DIAGNOSTICS_LEVEL_GOOD_INTEL (macro definition) of file nbnxm_ocl_data_mgmt.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_data_mgmt.cpp:90: warning: Member CL_CONTEXT_DIAGNOSTICS_LEVEL_BAD_INTEL (macro definition) of file nbnxm_ocl_data_mgmt.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_data_mgmt.cpp:91: warning: Member CL_CONTEXT_DIAGNOSTICS_LEVEL_NEUTRAL_INTEL (macro definition) of file nbnxm_ocl_data_mgmt.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:646: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:657: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:692: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:703: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:737: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:746: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:656: warning: Member Simd4NFloat (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:702: warning: Member Simd4NDouble (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:745: warning: Member Simd4NReal (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:518: warning: Member load(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:524: warning: Member load(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:542: warning: Member loadU(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:548: warning: Member loadU(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:627: warning: Member load(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:632: warning: Member loadU(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:661: warning: Member loadUNDuplicate4(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:665: warning: Member load4DuplicateN(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:669: warning: Member loadU4NOffset(const float *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:707: warning: Member loadUNDuplicate4(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:711: warning: Member load4DuplicateN(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:715: warning: Member loadU4NOffset(const double *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:380: warning: Member c_simdBestPairAlignment (variable) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/resourcedivision.cpp:116: warning: Member nthreads_omp_faster_Nehalem (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/resourcedivision.cpp:117: warning: Member nthreads_omp_faster_Intel_AVX (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/resourcedivision.cpp:118: warning: Member nthreads_omp_faster_AMD_Ryzen (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/resourcedivision.cpp:125: warning: Member nthreads_omp_faster_gpu_fac (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/resourcedivision.cpp:135: warning: Member nthreads_omp_mpi_ok_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/resourcedivision.cpp:136: warning: Member nthreads_omp_mpi_ok_min_cpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/resourcedivision.cpp:137: warning: Member nthreads_omp_mpi_ok_min_gpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/taskassignment/resourcedivision.cpp:138: warning: Member nthreads_omp_mpi_target_max (variable) of file resourcedivision.cpp is not documented. warning: Included by graph for 'arrayref.h' not generated, too many nodes (134), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (126), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/basedefinitions.h:178: warning: Member INTEL_DIAGNOSTIC_IGNORE(id) (macro definition) of file basedefinitions.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/basedefinitions.h:179: warning: Member INTEL_DIAGNOSTIC_RESET (macro definition) of file basedefinitions.h is not documented. warning: Included by graph for 'classhelpers.h' not generated, too many nodes (109), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'exceptions.h' not generated, too many nodes (178), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'fatalerror.h' not generated, too many nodes (77), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:200: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:201: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:202: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:203: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:204: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:205: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:206: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/fatalerror.h:207: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. warning: Included by graph for 'gmxassert.h' not generated, too many nodes (181), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:69: warning: Member c_int16ValueSwapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:70: warning: Member c_int32Value (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:71: warning: Member c_int32ValueSwapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:72: warning: Member c_int64Value (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:73: warning: Member c_int64ValueSwapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:75: warning: Member c_intAndFloat32 (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:76: warning: Member c_intAndFloat64 (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:78: warning: Member c_intAndFloat32Swapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:79: warning: Member c_intAndFloat64Swapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. warning: Included by graph for 'real.h' not generated, too many nodes (110), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'smalloc.h' not generated, too many nodes (103), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:192: warning: Member toString(bool t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:196: warning: Member toString(int t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:200: warning: Member toString(int64_t t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:204: warning: Member toString(float t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:208: warning: Member toString(double t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:212: warning: Member toString(std::string t) (function) of gmx is not documented. warning: Included by graph for 'stringutil.h' not generated, too many nodes (163), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/normalmodes.cpp:149: warning: Member integratorsToTest_g (variable) of gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/simple_mdrun.cpp:176: warning: Member md_g (variable) of gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. warning: Included by graph for 'cmdlinetest.h' not generated, too many nodes (50), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'refdata.h' not generated, too many nodes (73), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:95: warning: Member getCDataChildNode(XMLNodePtr node) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:105: warning: Member hasCDataContent(XMLNodePtr node) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:342: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:255: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:263: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:271: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:313: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:348: warning: Member createRootElement(XMLDocumentPtr document) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. warning: Included by graph for 'testasserts.h' not generated, too many nodes (117), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:380: warning: Member c_simdBestPairAlignment (variable) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:656: warning: Member Simd4NFloat (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:702: warning: Member Simd4NDouble (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:745: warning: Member Simd4NReal (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:518: warning: Member load(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:524: warning: Member load(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:542: warning: Member loadU(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:548: warning: Member loadU(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:627: warning: Member load(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:632: warning: Member loadU(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:661: warning: Member loadUNDuplicate4(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:665: warning: Member load4DuplicateN(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:669: warning: Member loadU4NOffset(const float *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:707: warning: Member loadUNDuplicate4(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:711: warning: Member load4DuplicateN(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:715: warning: Member loadU4NOffset(const double *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:646: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:657: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:692: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:703: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:737: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:746: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of group module_simd is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:452: warning: Member type (typedef) of struct gmx::internal::SimdTraits< SimdFloat > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:454: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< SimdFloat > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:461: warning: Member type (typedef) of struct gmx::internal::SimdTraits< SimdDouble > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:463: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< SimdDouble > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:470: warning: Member type (typedef) of struct gmx::internal::SimdTraits< SimdFInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:472: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< SimdFInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:479: warning: Member type (typedef) of struct gmx::internal::SimdTraits< SimdDInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:481: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< SimdDInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:488: warning: Member type (typedef) of struct gmx::internal::SimdTraits< const T > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:490: warning: Member tag (typedef) of struct gmx::internal::SimdTraits< const T > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:612: warning: Member type (typedef) of struct gmx::internal::Simd4Traits< Simd4Float > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:620: warning: Member type (typedef) of struct gmx::internal::Simd4Traits< Simd4Double > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:453: warning: Member width (variable) of struct gmx::internal::SimdTraits< SimdFloat > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:462: warning: Member width (variable) of struct gmx::internal::SimdTraits< SimdDouble > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:471: warning: Member width (variable) of struct gmx::internal::SimdTraits< SimdFInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:480: warning: Member width (variable) of struct gmx::internal::SimdTraits< SimdDInt32 > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:489: warning: Member width (variable) of struct gmx::internal::SimdTraits< const T > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_math.h:5052: warning: @copydetails or @copydoc target 'pow(SimdFloat)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:192: warning: Member toString(bool t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:196: warning: Member toString(int t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:200: warning: Member toString(int64_t t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:204: warning: Member toString(float t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:208: warning: Member toString(double t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:212: warning: Member toString(std::string t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:284: warning: Member kernel_noener_noprune_ptr[eelOclNR][evdwOclNR] (variable) of struct gmx_nbnxn_ocl_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:285: warning: Member kernel_ener_noprune_ptr[eelOclNR][evdwOclNR] (variable) of struct gmx_nbnxn_ocl_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:286: warning: Member kernel_noener_prune_ptr[eelOclNR][evdwOclNR] (variable) of struct gmx_nbnxn_ocl_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:287: warning: Member kernel_ener_prune_ptr[eelOclNR][evdwOclNR] (variable) of struct gmx_nbnxn_ocl_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:295: warning: Member kernel_memset_f (variable) of struct gmx_nbnxn_ocl_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:296: warning: Member kernel_memset_f2 (variable) of struct gmx_nbnxn_ocl_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:297: warning: Member kernel_memset_f3 (variable) of struct gmx_nbnxn_ocl_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:298: warning: Member kernel_zero_e_fshift (variable) of struct gmx_nbnxn_ocl_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:116: warning: Member ewaldcoeff_q (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:117: warning: Member ewaldcoeff_lj (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:132: warning: Member vir_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:133: warning: Member energy_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:134: warning: Member energy_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:135: warning: Member dvdlambda_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_pp_communication.h:136: warning: Member dvdlambda_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:115: warning: Member chargeB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:116: warning: Member sqrt_c6A (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:117: warning: Member sqrt_c6B (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:118: warning: Member sigmaA (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:119: warning: Member sigmaB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:126: warning: Member stat (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp:143: warning: Member cyclic (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp:144: warning: Member order (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp:145: warning: Member tmpswap (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp:146: warning: Member incycle (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp:147: warning: Member bEx (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp:153: warning: Member Epot (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp:154: warning: Member beta (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp:155: warning: Member Vol (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp:156: warning: Member de (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:65: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:66: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:67: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:68: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:72: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:111: warning: Member splineKernel (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:112: warning: Member splineKernelThPerAtom4 (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:113: warning: Member spreadKernel (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:114: warning: Member spreadKernelThPerAtom4 (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:115: warning: Member splineAndSpreadKernel (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:116: warning: Member splineAndSpreadKernelThPerAtom4 (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:117: warning: Member splineAndSpreadKernelWriteSplines (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:118: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4 (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:129: warning: Member gatherReduceWithInputKernel (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:130: warning: Member gatherReduceWithInputKernelThPerAtom4 (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:131: warning: Member gatherKernel (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:132: warning: Member gatherKernelThPerAtom4 (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:133: warning: Member gatherReduceWithInputKernelReadSplines (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:134: warning: Member gatherReduceWithInputKernelReadSplinesThPerAtom4 (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:135: warning: Member gatherKernelReadSplines (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:136: warning: Member gatherKernelReadSplinesThPerAtom4 (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:145: warning: Member solveYZXKernel (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:146: warning: Member solveXYZKernel (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:147: warning: Member solveYZXEnergyKernel (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.h:148: warning: Member solveXYZEnergyKernel (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:168: warning: Member nSkip (variable) of struct t_UmbrellaHeader is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:169: warning: Member Reference[256] (variable) of struct t_UmbrellaHeader is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:170: warning: Member nPull (variable) of struct t_UmbrellaHeader is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:171: warning: Member nDim (variable) of struct t_UmbrellaHeader is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:172: warning: Member Dims (variable) of struct t_UmbrellaHeader is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:173: warning: Member PullName[4][256] (variable) of struct t_UmbrellaHeader is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:174: warning: Member UmbPos[4][3] (variable) of struct t_UmbrellaHeader is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:175: warning: Member UmbCons[4][3] (variable) of struct t_UmbrellaHeader is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:232: warning: Member fnTpr (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:232: warning: Member fnPullf (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:232: warning: Member fnCoordSel (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:233: warning: Member fnPdo (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:234: warning: Member bTpr (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:234: warning: Member bPullf (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:234: warning: Member bPdo (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:235: warning: Member tmin (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:235: warning: Member tmax (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:247: warning: Member min (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:247: warning: Member max (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:247: warning: Member dz (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:248: warning: Member Temperature (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:264: warning: Member bBoundsOnly (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:275: warning: Member bTauIntGiven (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:286: warning: Member bHistEq (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:312: warning: Member bsMethod (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:315: warning: Member tauBootStrap (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:319: warning: Member histBootStrapBlockLength (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:325: warning: Member bs_verbose (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:331: warning: Member bTab (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:332: warning: Member tabX (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:332: warning: Member tabY (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:332: warning: Member tabMin (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:332: warning: Member tabMax (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:332: warning: Member tabDz (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp:333: warning: Member tabNbins (variable) of struct t_UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/vsite_parm.cpp:89: warning: Member aj() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/vsite_parm.cpp:90: warning: Member ak() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/vsite_parm.cpp:91: warning: Member al() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gmxpreprocess/vsite_parm.cpp:93: warning: Member parameterValue() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/indexutil.cpp:92: warning: Member setGroup(const int(&atoms)[count]) (function) of class anonymous_namespace{indexutil.cpp}::IndexBlockTest is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClCommandQueue (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClProgram (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/oclraii.h:134: warning: Member ClKernel (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/vec.h:635: warning: Member norm2(T *v) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:192: warning: Member toString(bool t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:196: warning: Member toString(int t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:200: warning: Member toString(int64_t t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:204: warning: Member toString(float t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:208: warning: Member toString(double t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/strconvert.h:212: warning: Member toString(std::string t) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:380: warning: Member c_simdBestPairAlignment (variable) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:656: warning: Member Simd4NFloat (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:702: warning: Member Simd4NDouble (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:745: warning: Member Simd4NReal (typedef) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:518: warning: Member load(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:524: warning: Member load(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:542: warning: Member loadU(const std::enable_if_t< std::is_arithmetic< T >::value, T > *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:548: warning: Member loadU(const AlignedArray< typename internal::SimdTraits< T >::type, N > &m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:627: warning: Member load(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:632: warning: Member loadU(const typename internal::Simd4Traits< T >::type *m) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:661: warning: Member loadUNDuplicate4(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:665: warning: Member load4DuplicateN(const float *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:669: warning: Member loadU4NOffset(const float *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:707: warning: Member loadUNDuplicate4(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:711: warning: Member load4DuplicateN(const double *f) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd.h:715: warning: Member loadU4NOffset(const double *f, int) (function) of gmx is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:251: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/arrayref.h:259: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:118: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:125: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:132: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:139: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:146: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:153: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:160: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:167: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copybrief or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copybrief or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/densityfittingforce.cpp:67: warning: @copydetails or @copydoc target 'DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan densityDerivative)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:346: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:348: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:349: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:351: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:352: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:354: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:355: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:357: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/math/paddedvector.h:358: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/lincs.cpp:204: warning: Member tmpncc (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/lincs.cpp:205: warning: Member tmp1 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/lincs.cpp:206: warning: Member tmp2 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/lincs.cpp:207: warning: Member tmp3 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdlib/lincs.cpp:208: warning: Member tmp4 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:140: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:143: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:145: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:148: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:149: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:150: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:151: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:152: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:153: warning: Member gpuIdsAvailable (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:154: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:157: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/legacymdrunoptions.h:159: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/runner.h:148: warning: Member operator=(Mdrunner &&handle) noexcept(BUGFREE_NOEXCEPT_STRING) (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/mdrun/runner.h:376: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/basicoptionstorage.h:75: warning: Member formatSingleValue(const bool &value) const override (function) of class gmx::BooleanOptionStorage is not documented. :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:325: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< bool > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/basicoptionstorage.h:97: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::IntegerOptionStorage is not documented. :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:325: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/basicoptionstorage.h:117: warning: Member formatSingleValue(const int64_t &value) const override (function) of class gmx::Int64OptionStorage is not documented. :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:325: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int64_t > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/basicoptionstorage.h:136: warning: Member formatSingleValue(const double &value) const override (function) of class gmx::DoubleOptionStorage is not documented. :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:325: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< double > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/basicoptionstorage.h:164: warning: Member formatSingleValue(const float &value) const override (function) of class gmx::FloatOptionStorage is not documented. :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:325: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< float > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:325: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/basicoptionstorage.h:238: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::EnumOptionStorage is not documented. :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:325: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:325: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/manager.h:90: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/manager.h:91: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/manager.h:92: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/restraintmdmodule.h:89: warning: argument 'restraint' from the argument list of gmx::RestraintMDModule::create has multiple @param documentation sections /build/reproducible-path/gromacs-2020.6/src/gromacs/restraint/restraintmdmodule_impl.h:288: warning: Member operator=(RestraintMDModuleImpl &&) noexcept=default (function) of class gmx::RestraintMDModuleImpl is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:105: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/options/optionstoragetemplate.h:107: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/symrec.h:151: warning: Member iterator_category (typedef) of class gmx::SelectionParserSymbolIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/symrec.h:152: warning: Member value_type (typedef) of class gmx::SelectionParserSymbolIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/symrec.h:153: warning: Member difference_type (typedef) of class gmx::SelectionParserSymbolIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/symrec.h:154: warning: Member pointer (typedef) of class gmx::SelectionParserSymbolIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/symrec.h:155: warning: Member reference (typedef) of class gmx::SelectionParserSymbolIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:117: warning: Member iterator_category (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:118: warning: Member value_type (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:119: warning: Member difference_type (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:120: warning: Member pointer (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:121: warning: Member reference (typedef) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:158: warning: Member operator!=(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:162: warning: Member operator<(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:166: warning: Member operator>(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:170: warning: Member operator<=(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:174: warning: Member operator>=(const EnumerationIterator other) const noexcept (function) of class gmx::EnumerationIterator is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:210: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:274: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:275: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:276: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:298: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:253: warning: Member operator[](const std::size_t index) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:259: warning: Member operator[](const EnumType index) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:264: warning: Member operator[](const EnumType index) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:282: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:283: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:284: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:290: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:291: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/enumerationhelpers.h:292: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:78: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:79: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:80: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:81: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:82: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:83: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:84: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:85: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:86: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:87: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:88: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:89: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:90: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:104: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:111: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:118: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:125: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:132: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:139: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:146: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:153: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:160: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:167: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/iserializer.h:174: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/gpu_utils/clfftinitializer.cpp:70: warning: Member g_clfftMutex (variable) of gmx::anonymous_namespace{clfftinitializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/applied_forces/electricfield.cpp:170: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:179: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:185: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:191: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:197: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:203: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of gmx::compat is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:117: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:118: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:129: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/compat/pointers.h:130: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/simd/simd_memory.h:207: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:74: warning: Member requestVelocities() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:75: warning: Member requestForces() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:76: warning: Member initFrameIndices(const ArrayRef< const int > &index) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:87: warning: Member initAtomTypes(const ArrayRef< const char *const > &types) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:88: warning: Member initUniformResidues(int residueSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:89: warning: Member initUniformMolecules(int moleculeSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:105: warning: Member setMoleculeType(int moleculeTypeIndex, ArrayRef< const int > residueSizes) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:106: warning: Member setMoleculeBlock(int moleculeBlockIndex, int moleculeTypeIndex, int numMoleculesToAdd) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:107: warning: Member finalizeTopology() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:113: warning: Member atoms() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/selection/tests/toputils.h:114: warning: Member frame() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:136: warning: Member topFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:137: warning: Member groFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:138: warning: Member fullPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:139: warning: Member reducedPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:140: warning: Member groOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:141: warning: Member ndxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:142: warning: Member mdpOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:143: warning: Member tprFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:144: warning: Member logFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:145: warning: Member edrFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:146: warning: Member mtxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:147: warning: Member cptFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:148: warning: Member swapFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/moduletest.h:149: warning: Member nsteps_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/trajectorycomparison.h:62: warning: Member coordinates (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/trajectorycomparison.h:62: warning: Member velocities (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/trajectorycomparison.h:62: warning: Member forces (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp:72: warning: Member c_int32Value (variable) of gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp:73: warning: Member c_int64Value (variable) of gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp:75: warning: Member c_intAndFloat32 (variable) of gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp:76: warning: Member c_intAndFloat64 (variable) of gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:69: warning: Member c_int16ValueSwapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:70: warning: Member c_int32Value (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:71: warning: Member c_int32ValueSwapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:72: warning: Member c_int64Value (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:73: warning: Member c_int64ValueSwapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:75: warning: Member c_intAndFloat32 (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:76: warning: Member c_intAndFloat64 (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:78: warning: Member c_intAndFloat32Swapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp:79: warning: Member c_intAndFloat64Swapped (variable) of gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp:169: warning: Member minimizersToTest_g (variable) of gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp:171: warning: Member constrainedSystemsToTest_g (variable) of gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp:173: warning: Member minimizersToTestWithConstraints_g (variable) of gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/normalmodes.cpp:149: warning: Member integratorsToTest_g (variable) of gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:95: warning: Member getCDataChildNode(XMLNodePtr node) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:105: warning: Member hasCDataContent(XMLNodePtr node) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:342: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:255: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:263: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:271: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:313: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/testutils/refdata_xml.cpp:348: warning: Member createRootElement(XMLDocumentPtr document) (function) of gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2020.6/src/programs/mdrun/tests/simple_mdrun.cpp:176: warning: Member md_g (variable) of gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/doxygen-full-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [100%] Built target doxygen-full /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2020.6/build/documentation/docs/doxygen/CMakeFiles/doxygen-all.dir/DependInfo.cmake --color= Scanning dependencies of target doxygen-all make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[4]: Nothing to be done for 'docs/doxygen/CMakeFiles/doxygen-all.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [100%] Built target doxygen-all /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/docs /build/reproducible-path/gromacs-2020.6/build/documentation /build/reproducible-path/gromacs-2020.6/build/documentation/docs /build/reproducible-path/gromacs-2020.6/build/documentation/docs/CMakeFiles/webpage.dir/DependInfo.cmake --color= Scanning dependencies of target webpage make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/documentation' cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E echo "webpage was built, but with the following limitations:" webpage was built, but with the following limitations: cd /build/reproducible-path/gromacs-2020.6/build/documentation/docs && /usr/bin/cmake -E echo " - Reference PDF manual was not built, so links to it do not work" - Reference PDF manual was not built, so links to it do not work make[4]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' [100%] Built target webpage make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/documentation' dh_testdir dh_testroot dh_prep -pgromacs dh_installdirs -pgromacs /usr/bin/make -j16 -C build/basic install DESTDIR=/build/reproducible-path/gromacs-2020.6/debian/gromacs make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build [ 0%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 0%] Built target release-version-info make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 1%] Built target lmfit_objlib [ 1%] Built target tng_io_obj [ 5%] Built target thread_mpi /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend [ 6%] Built target linearalgebra [ 8%] Built target modularsimulator make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 8%] Built target vmddlopen /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 10%] Built target mdrun_objlib /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 11%] Built target view_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/share/template /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/share/template /build/reproducible-path/gromacs-2020.6/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/programs /build/reproducible-path/gromacs-2020.6/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' cd /build/reproducible-path/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [ 98%] Built target gmx make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'share/template/CMakeFiles/template.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' [100%] Built target gmxapi [100%] Built target template make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmeig.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mk_angndx.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-spatial.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dielectric.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sasa.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dipoles.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-solvate.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-polystat.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-covar.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-analyze.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-freevolume.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-filter.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sans.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rmsdist.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mdrun.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-chi.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-order.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-report-methods.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmtraj.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmr.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-pdb2gmx.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sigeps.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-velacc.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-msd.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-saxs.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-trjorder.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-trjconv.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-helixorient.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-confrms.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-gangle.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-spol.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sham.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-make_ndx.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-insert-molecules.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-traj.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-pairdist.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-convert-trj.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-help.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-genconf.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-view.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-extract-cluster.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rms.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dos.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-density.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-bar.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-principal.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-x2top.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-tune_pme.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sorient.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-check.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dyecoupl.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-convert-tpr.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-xpm2ps.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-h2order.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-editconf.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-distance.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-disre.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mindist.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rama.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-densorder.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-densmap.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmens.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-genion.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mdmat.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rotmat.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-tcaf.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-grompp.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-anaeig.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-enemat.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-vanhove.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-trajectory.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-genrestr.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-hydorder.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-hbond.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-gyrate.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-angle.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-select.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-eneconv.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dump.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-saltbr.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rdf.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-helix.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rotacf.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-wham.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-awh.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-wheel.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-lie.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-clustsize.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rmsf.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-potential.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-energy.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-trjcat.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-bundle.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-cluster.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-current.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-do_dssp.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-pme_error.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-make_edi.1 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/README.tutor -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/electroneg.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber94.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/phbres.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ffoplsaa-n.tst -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ffG43a1.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/elements.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/residues.xml -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/bonds.dlg -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/atom_nom.tbl -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/table6-9.xvg -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/edissoc.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ffG53a5.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/sw.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/cb-shift.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/flexspc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ffG45a3.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/tip5p.gro -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/surface.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/specbond.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/spc216.gro -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/residues.dtd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ffoplsaa.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/flexwat-ferguson.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/table6-11.xvg -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/random.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ca-shift.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ss.map -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/sfactor.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/README -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amberGS.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ffG53a6.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ffG43a2.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ps.m2p -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/vdw-msms.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/flexspce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/residuetypes.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/xlateat.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/table6-8.xvg -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/co-shift.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/tip4p.gro -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber03.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/atommass.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ha-shift.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/export.dlg -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/defselection.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/table6-12.xvg -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/vdwradii.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/table6-10.xvg -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/nsfactor.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/dgsolv.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/template/CMakeLists.txt -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/template/README -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/template/template.cpp -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/template/Makefile.pkg -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/template/cmake/FindGROMACS.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC.csh -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/demux.pl -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/version.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/trajectoryanalysis.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgromacs.so.5.0.0 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgromacs.so.5 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgromacs.so -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/pkgconfig/libgromacs.pc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs/gromacs-config.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs/gromacs-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs/gromacs-toolchain.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/current_function.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/real.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/arrayref.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/baseversion.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/classhelpers.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/enumerationhelpers.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/exceptions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/fileptr.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/futil.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/flags.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/pleasecite.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/programcontext.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/range.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/smalloc.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/stringutil.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/unique_cptr.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/do_fit.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/functions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/units.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/utilities.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/vec.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/vectypes.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/do_fit.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/units.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/utilities.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/mdtypes/inputrec.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/mdtypes/md_enums.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/abstractoption.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/basicoptions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/filenameoption.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/filenameoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/ioptionsbehavior.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/ioptionscontainer.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/ioptionscontainerwithsections.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/ivaluestore.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/optionfiletype.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/optionflags.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/options.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/options/timeunitmanager.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/pbcutil/pbc.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/topology/atomprop.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/topology/atoms.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/topology/block.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/topology/forcefieldparameters.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/topology/idef.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/topology/ifunc.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/topology/index.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/topology/symtab.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/topology/topology.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/trajectory/trajectoryframe.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/abstractdata.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/analysisdata.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/arraydata.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/dataframe.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/datamodule.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/modules/average.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/modules/displacement.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/modules/histogram.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/modules/lifetime.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/analysisdata/modules/plot.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysismodule.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysissettings.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/trajectoryanalysis/topologyinformation.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/fileio/oenv.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/fileio/confio.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/fileio/pdbio.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/fileio/tpxio.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/fileio/trxio.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/fileio/filetypes.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection/indexutil.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection/nbsearch.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection/position.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection/selectioncollection.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection/selectionenums.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection/selection.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection/selectionoptionbehavior.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection/selectionoption.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/selection/selectionoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/gmx -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/gmx-completion-gmx.bash -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/session.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/context.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/gromacsfwd.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/md -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/md/mdsignals.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/md/mdmodule.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/session -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/session/resources.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/status.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/compat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/compat/tpr.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/compat/mdparams.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/md.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/gmxapi.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/exceptions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgmxapi.so.0.1.0 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgmxapi.so.0 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgmxapi.so -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gmxapi/gmxapi-config.cmake make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic' /usr/bin/make -j16 -C build/basic-dp install DESTDIR=/build/reproducible-path/gromacs-2020.6/debian/gromacs make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 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make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 1%] Built target scanner /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 1%] Built target lmfit_objlib [ 5%] Built target thread_mpi [ 6%] Built target tng_io_obj /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend [ 6%] Built target release-version-info /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= [ 6%] Built target linearalgebra make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator 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'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 8%] Built target modularsimulator [ 8%] Built target vmddlopen /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 10%] Built target view_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' cd /build/reproducible-path/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic-dp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp /build/reproducible-path/gromacs-2020.6/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build [ 98%] Built target gmx make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' [100%] Built target gmxapi make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sans.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: 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/build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Up-to-date: 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/build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/vdw-msms.dat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/flexspce.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: 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/build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/dgsolv.dat -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgromacs_d.so.5.0.0 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgromacs_d.so.5 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgromacs_d.so -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/pkgconfig/libgromacs_d.pc -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs_d/gromacs_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs_d/gromacs_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gromacs_d/gromacs-toolchain_d.cmake -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/basedefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/current_function.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/gmxassert.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/utility/real.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/do_fit.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/functions.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/units.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/utilities.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/vec.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/vectypes.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/gmx_d -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/gmx-completion-gmx_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/gmxapicompat.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/exceptions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgmxapi_d.so.0.1.0 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgmxapi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/libgmxapi_d.so -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake/gmxapi/gmxapi-config.cmake make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/basic-dp' dh_installman -pgromacs debian/man/demux.1 debian/man/xplor2gmx.1 # gmx(1) -> gmx_d(1) dh_link -pgromacs -pgromacs-data dh_testdir dh_testroot dh_prep -pgromacs-mpich dh_installdirs -pgromacs-mpich /usr/bin/make -j16 -C build/mpich install DESTDIR=/build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/mpich/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/mpich//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/mpich/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/mpich/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build [ 0%] Built target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [ 0%] Built target scanner [ 0%] Built target lmfit_objlib [ 2%] Built target tng_io_obj [ 4%] Built target thread_mpi [ 4%] Built target linearalgebra [ 7%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend [ 8%] Built target mdrun_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [100%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' cd /build/reproducible-path/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich /build/reproducible-path/gromacs-2020.6/build/mpich/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' [100%] Built target mdrun make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/mpich/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/current_function.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/real.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/do_fit.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/functions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/units.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/utilities.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/vec.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/vectypes.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/bin/mdrun_mpi.mpich -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi.mpich.bash make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich' /usr/bin/make -j16 -C build/mpich-dp install DESTDIR=/build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/mpich-dp/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/mpich-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/mpich-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/mpich-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' [ 0%] Built target scanner [ 0%] Built target release-version-info make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build [ 1%] Built target thread_mpi make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' [ 4%] Built target tng_io_obj [ 7%] Built target modularsimulator [ 7%] Built target linearalgebra /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend [ 8%] Built target mdrun_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' [100%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' cd /build/reproducible-path/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich-dp /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/mpich-dp/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/mpich-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/basedefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/current_function.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/gmxassert.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/real.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/do_fit.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/functions.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/units.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/utilities.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/vec.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/vectypes.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/bin/mdrun_mpi_d.mpich -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi_d.mpich.bash make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/mpich-dp' # overlapping include files with libgromacs-dev: temporary fix as of 2020-beta1 rm -rf /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/include chmod 644 /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion* mv /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi.mpich.bash /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi.mpich mv /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi_d.mpich.bash /build/reproducible-path/gromacs-2020.6/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi_d.mpich dh_installman -pgromacs-mpich debian/man/mdrun_mpi.mpich.1 dh_link -pgromacs-mpich usr/share/man/man1/mdrun_mpi.mpich.1.gz usr/share/man/man1/mdrun_mpi_d.mpich.1.gz dh_lintian -pgromacs-mpich dh_testdir dh_testroot dh_prep -pgromacs-openmpi dh_installdirs -pgromacs-openmpi /usr/bin/make -j16 -C build/openmpi install DESTDIR=/build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/openmpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/openmpi/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/openmpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/openmpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/openmpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 0%] Built target scanner /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend [ 1%] Built target thread_mpi [ 4%] Built target tng_io_obj [ 4%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= [ 4%] Built target release-version-info make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [ 5%] Built target mdrun_objlib [ 5%] Built target linearalgebra [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [100%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' cd /build/reproducible-path/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi /build/reproducible-path/gromacs-2020.6/build/openmpi/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' [100%] Built target mdrun make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/openmpi/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/current_function.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/real.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/do_fit.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/functions.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/units.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/utilities.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/vec.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/vectypes.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/mdrun_mpi.openmpi -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi.openmpi.bash make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi' /usr/bin/make -j16 -C build/openmpi-dp install DESTDIR=/build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi make[1]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2020.6 -B/build/reproducible-path/gromacs-2020.6/build/openmpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/CMakeFiles /build/reproducible-path/gromacs-2020.6/build/openmpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2020.6/build/openmpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/reproducible-path/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [ 0%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build [ 0%] Built target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend [ 0%] Built target linearalgebra make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= [ 1%] Built target thread_mpi cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= [ 4%] Built target tng_io_obj make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 5%] Built target mdrun_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [100%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' cd /build/reproducible-path/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2020.6 /build/reproducible-path/gromacs-2020.6/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/programs /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2020.6/build/openmpi-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/basedefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/current_function.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/gmxassert.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/real.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/do_fit.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/functions.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/units.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/utilities.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/vec.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/vectypes.h -- Up-to-date: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/mdrun_mpi_d.openmpi -- Installing: /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi_d.openmpi.bash make[1]: Leaving directory '/build/reproducible-path/gromacs-2020.6/build/openmpi-dp' # overlapping include files with libgromacs-dev: temporary fix as of 2020-beta1 rm -rf /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/include chmod 644 /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion* mv /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi.openmpi.bash /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi.openmpi mv /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi_d.openmpi.bash /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi_d.openmpi # Force-disable RUNPATH - see # and lintian tag binary-or-shlib-defines-rpath in versions >= 2.5.50 chrpath -d /build/reproducible-path/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/mdrun_mpi* dh_installman -pgromacs-openmpi debian/man/mdrun_mpi.openmpi.1 dh_link -pgromacs-openmpi usr/share/man/man1/mdrun_mpi.openmpi.1.gz usr/share/man/man1/mdrun_mpi_d.openmpi.1.gz dh_lintian -pgromacs-openmpi dh_testdir dh_testroot dh_prep -pgromacs-data -plibgromacs-dev dh_installdirs -pgromacs-data mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top \ /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/gromacs mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/man \ /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/man # some of the default installation directories for documentation and # example shell scripts are not FHS-friendly; move them appropriately perl -lne 'print' /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/gmx*.bash > \ /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/bash-completion/completions/gmx rm -f /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC* /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/gmx*.bash # symlinks, primarily for /usr/share/doc/{gromacs,libgromacs*} -> gromacs-data dh_link -pgromacs-data # rename a pair of Perl scripts to drop the .pl extension (Policy 10.4) mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/demux.pl /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/demux mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/xplor2gmx.pl /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/bin/xplor2gmx mkdir -p /build/reproducible-path/gromacs-2020.6/debian/libgromacs5/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/*/*.so.* /build/reproducible-path/gromacs-2020.6/debian/libgromacs5/usr/lib/x86_64-linux-gnu/ dh_installdirs -plibgromacs-dev mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/include /build/reproducible-path/gromacs-2020.6/debian/libgromacs-dev/usr/include # catch normal libraries plus all applicable MPI variants mkdir -p /build/reproducible-path/gromacs-2020.6/debian/libgromacs-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/*.so \ /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/pkgconfig \ /build/reproducible-path/gromacs-2020.6/debian/libgromacs-dev/usr/lib/x86_64-linux-gnu/ rmdir /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/lib mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/template /build/reproducible-path/gromacs-2020.6/debian/libgromacs-dev/usr/share/gromacs/template # remaining documentation catch-all mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs/* /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs rmdir /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/gromacs # what are you doing here? mv /build/reproducible-path/gromacs-2020.6/debian/gromacs/usr/share/cmake /build/reproducible-path/gromacs-2020.6/debian/libgromacs-dev/usr/share/gromacs/ dh_lintian -pgromacs -pgromacs-data -plibgromacs5 dh_testdir dh_testroot dh_install -pgromacs-data dh_installman -pgromacs-data /build/reproducible-path/gromacs-2020.6/build/documentation/docs/man/*.[1-9] # dh_doxygen expects a different location of index.html, so do its cleanup manually. find /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/ -type f -a \( -name '*.md5' -o -name '*.map' \) -delete rdfind -outputname /dev/null -makesymlinks true /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/ Now scanning "/build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc", found 19015 files. Now have 19015 files in total. Removed 0 files due to nonunique device and inode. Total size is 225043760 bytes or 215 MiB Removed 6587 files due to unique sizes from list.12428 files left. Now eliminating candidates based on first bytes:removed 2877 files from list.9551 files left. Now eliminating candidates based on last bytes:removed 1129 files from list.8422 files left. Now eliminating candidates based on sha1 checksum:removed 2167 files from list.6255 files left. It seems like you have 6255 files that are not unique Totally, 20 MiB can be reduced. Now making results file /dev/null Now making symbolic links. creating Making 3671 links. symlinks -r -s -c /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/ dangling: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs-data/COPYING -> copyright absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/jquery.js changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> ../html-full/jquery.js absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/trajectoryanalysis_8h__incl.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/trajectoryanalysis_8h__incl.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/trajectoryanalysis_8h__incl.svg -> ../html-full/trajectoryanalysis_8h__incl.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/template_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> ../html-full/template_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h__incl.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputadapters_8h__incl.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h__incl.svg -> ../html-full/outputadapters_8h__incl.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/position_8h.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/position_8h.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/position_8h.xhtml -> ../html-lib/position_8h.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64General.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/random_8h__incl.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/random_8h__incl.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/random_8h__incl.svg -> ../html-full/random_8h__incl.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution.xhtml changed: 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/build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_8.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_8.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_8.xhtml -> ../../html-full/search/defines_8.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_a.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_a.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_a.xhtml -> ../../html-full/search/defines_a.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_b.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/classes_b.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_b.xhtml -> ../../html-full/search/classes_b.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_f.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/classes_f.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_f.xhtml -> ../../html-full/search/classes_f.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_3.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/classes_3.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_3.xhtml -> ../../html-full/search/classes_3.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_6.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_6.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_6.xhtml -> ../../html-full/search/defines_6.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_5.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_5.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_5.xhtml -> ../../html-full/search/defines_5.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/files_11.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/files_11.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/files_11.xhtml -> ../../html-full/search/files_11.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_b.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_b.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_b.xhtml -> ../../html-full/search/groups_b.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/files_10.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/files_10.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/files_10.xhtml -> ../../html-full/search/files_10.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_3.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_3.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_3.xhtml -> ../../html-full/search/groups_3.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_5.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_5.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_5.xhtml -> ../../html-full/search/groups_5.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_1.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_1.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_1.xhtml -> ../../html-full/search/groups_1.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_2.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_2.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_2.xhtml -> ../../html-full/search/groups_2.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/files_12.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/files_12.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/files_12.xhtml -> ../../html-full/search/files_12.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_9.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_9.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_9.xhtml -> ../../html-full/search/groups_9.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_c.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_c.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_c.xhtml -> ../../html-full/search/groups_c.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_8.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_8.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_8.xhtml -> ../../html-full/search/groups_8.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_0.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_0.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_0.xhtml -> ../../html-full/search/groups_0.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_7.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_7.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_7.xhtml -> ../../html-full/search/groups_7.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_4.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_4.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_4.xhtml -> ../../html-full/search/groups_4.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_6.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_6.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_6.xhtml -> ../../html-full/search/groups_6.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_a.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_a.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/groups_a.xhtml -> ../../html-full/search/groups_a.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_0.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_0.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_0.xhtml -> ../../html-full/search/pages_0.xhtml absolute: 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/build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_e.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_e.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_e.xhtml -> ../../html-full/search/enums_e.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/files_c.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/files_c.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/files_c.xhtml -> ../../html-full/search/files_c.xhtml absolute: 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/build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_b.xhtml -> ../../html-full/search/related_b.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_0.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_0.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_0.xhtml -> ../../html-full/search/defines_0.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_e.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_e.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_e.xhtml -> ../../html-full/search/defines_e.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_1.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_1.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_1.xhtml -> ../../html-full/search/defines_1.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_b.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_b.xhtml changed: 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/build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_8.xhtml -> ../../html-full/search/pages_8.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_7.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_7.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_7.xhtml -> ../../html-full/search/enums_7.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_3.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_3.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_3.xhtml -> ../../html-full/search/pages_3.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_c.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_c.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_c.xhtml -> ../../html-full/search/enums_c.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/files_d.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/files_d.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/files_d.xhtml -> ../../html-full/search/files_d.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_1.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_1.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_1.xhtml -> ../../html-full/search/enums_1.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_a.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_a.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_a.xhtml -> ../../html-full/search/pages_a.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_3.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_3.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_3.xhtml -> ../../html-full/search/enums_3.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_2.xhtml -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_2.xhtml changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_2.xhtml -> ../../html-full/search/pages_2.xhtml absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_a.xhtml -> 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/build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__inherit__graph.svg -> classgmx_1_1SetAtoms__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAnalysisTemplate__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAnalysisTemplate__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAnalysisTemplate__inherit__graph.svg -> classAnalysisTemplate__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__inherit__graph.svg -> classgmx_1_1SetBox__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1Simd4Test__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1Simd4Test__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1Simd4Test__inherit__graph.svg -> 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/build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSection__inherit__graph.svg -> classgmx_1_1OptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__inherit__graph.svg -> classgmx_1_1StandardInputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__inherit__graph.svg -> 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/build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__inherit__graph.svg -> classgmx_1_1InternalError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__inherit__graph.svg -> classgmx_1_1AnalysisData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__inherit__graph.svg -> classgmx_1_1StringInputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__inherit__graph.svg -> classgmx_1_1FileIOError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__inherit__graph.svg -> classgmx_1_1RestraintMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SwapCoordinates__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SwapCoordinates__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SwapCoordinates__inherit__graph.svg -> classgmx_1_1SwapCoordinates__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__inherit__graph.svg -> classgmx_1_1TextInputFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.svg -> /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.svg -> classgmx_1_1TextOutputFile__coll__graph.svg dh_testdir dh_testroot dh_installchangelogs -i dh_installdocs -pgromacs-data dh_strip_nondeterminism -i dh_compress -i -X.pdf dh_fixperms -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'gromacs-data' in '../gromacs-data_2020.6-2_all.deb'. dh_testdir -a dh_testroot -a dh_installchangelogs -a dh_installdocs -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_dwz -a dwz: debian/libgromacs5/usr/lib/x86_64-linux-gnu/libgromacs.so.5.0.0: DWARF compression not beneficial - old size 92125610 new size 92394334 dwz: debian/libgromacs5/usr/lib/x86_64-linux-gnu/libgromacs_d.so.5.0.0: DWARF compression not beneficial - old size 95629356 new size 95923404 dh_strip -A dh_makeshlibs -a dh_shlibdeps -plibgromacs5 -L libgromacs5 -l debian/libgromacs5/usr/lib dh_shlibdeps -pgromacs -L libgromacs5 -l debian/libgromacs5/usr/lib:debian/gromacs/usr/lib dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_installdeb -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gromacs' in '../gromacs_2020.6-2_amd64.deb'. dpkg-deb: building package 'libgromacs5-dbgsym' in '../libgromacs5-dbgsym_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs-openmpi-dbgsym' in '../gromacs-openmpi-dbgsym_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2020.6-2_amd64.deb'. dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs-mpich' in '../gromacs-mpich_2020.6-2_amd64.deb'. dpkg-deb: building package 'libgromacs5' in '../libgromacs5_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs-openmpi' in '../gromacs-openmpi_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs-mpich-dbgsym' in '../gromacs-mpich-dbgsym_2020.6-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gromacs_2020.6-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3709870 and its subdirectories I: Current time: Fri Feb 7 21:48:46 -12 2025 I: pbuilder-time-stamp: 1739008126 Sun Jan 7 03:25:47 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Sun Jan 7 03:25:47 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Sun Jan 7 05:03:11 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Sun Jan 7 05:03:11 UTC 2024 I: gromacs_2020.6-2_amd64.changes: Format: 1.8 Date: Sun, 28 Mar 2021 21:45:03 -0700 Source: gromacs Binary: gromacs gromacs-data gromacs-dbgsym gromacs-mpich gromacs-mpich-dbgsym gromacs-openmpi gromacs-openmpi-dbgsym libgromacs-dev libgromacs5 libgromacs5-dbgsym Architecture: all amd64 Version: 2020.6-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Nicholas Breen Description: gromacs - Molecular dynamics simulator, with building and analysis tools gromacs-data - GROMACS molecular dynamics sim, data and documentation gromacs-mpich - Molecular dynamics sim, binaries for MPICH parallelization gromacs-openmpi - Molecular dynamics sim, binaries for OpenMPI parallelization libgromacs-dev - GROMACS molecular dynamics sim, development kit libgromacs5 - GROMACS molecular dynamics sim, shared libraries Closes: 985157 Changes: gromacs (2020.6-2) unstable; urgency=medium . * Append newlines when concatenating bash completions. (Closes: #985157) Checksums-Sha1: 891c02bb1510d764fb7c578226c45180141f1d00 20581692 gromacs-data_2020.6-2_all.deb 7cca7fd5cb15c48a8af1b0d5d10c89ca5807df70 821244 gromacs-dbgsym_2020.6-2_amd64.deb db363e362841a9039ca6dec58e503b963908dc38 85051644 gromacs-mpich-dbgsym_2020.6-2_amd64.deb 90eef201c616182b02a1ce1ff493619caa4e79fa 6863660 gromacs-mpich_2020.6-2_amd64.deb a378740a79127a055ab2490c9b63bfb4a4291f27 85056096 gromacs-openmpi-dbgsym_2020.6-2_amd64.deb f997bb67b47b989d11427ca10956d0112e733d10 6868232 gromacs-openmpi_2020.6-2_amd64.deb 2285fd16b5efc1801b68e009416334a8bfa81605 15991 gromacs_2020.6-2_amd64.buildinfo 82efeeee60bcfc7b983926c7e971895c8af96ba7 137236 gromacs_2020.6-2_amd64.deb 7c14f38dad5244869f2ff597e2ea808803134a50 187296 libgromacs-dev_2020.6-2_amd64.deb ca9a858f116ed5dc46c3430bae76ad99adebe92d 121103916 libgromacs5-dbgsym_2020.6-2_amd64.deb c39d52e4959f0469d771dad6b09664add32baa80 11495956 libgromacs5_2020.6-2_amd64.deb Checksums-Sha256: 33cf8f47a9fd864a447fc41bf9cb06b790b8a903217ad6640e65ad296b51cd1a 20581692 gromacs-data_2020.6-2_all.deb 56cf89ae30abe7daebf84b6cfd04f56c5cec542aa628f1e2e87f6d7a5ae6f912 821244 gromacs-dbgsym_2020.6-2_amd64.deb bbca34e62ee8be585320158a9550e0e85f158f9f45f5458acdc09cbc788f697c 85051644 gromacs-mpich-dbgsym_2020.6-2_amd64.deb 98569fa8fe89262454a2b5043790c51866f10836f5c1368f17318eb8f8559ef2 6863660 gromacs-mpich_2020.6-2_amd64.deb aa6e1584800dcaa1a4c7b2151e4b42b18e08a9e39c82adc40a554815343f09de 85056096 gromacs-openmpi-dbgsym_2020.6-2_amd64.deb 9901e34151702ee90e8761db320c979ddcd3932bd9dd1ebef2ffcdfd3230f7dc 6868232 gromacs-openmpi_2020.6-2_amd64.deb 5f06a66d199b37c95c47e6d820764abd4346b2ee1cc7f5e8ad3a03f88b421c58 15991 gromacs_2020.6-2_amd64.buildinfo 25bb5e879f2b46269d9d6febf9c9b1139e6ca7d08d7f90020df2739ef960ec1e 137236 gromacs_2020.6-2_amd64.deb b839e860595ef9a1bf162b90456ceceadbf20b3908f1ea764a028d32cf986be2 187296 libgromacs-dev_2020.6-2_amd64.deb 04360421566f339a161ecb0d53b863abc3c09abf3157bf4e9a8dcf766bf99413 121103916 libgromacs5-dbgsym_2020.6-2_amd64.deb 7a08212cb2acdfd189c96094308179f5c6d9ade9a74c40b96c5e379fe0c30dde 11495956 libgromacs5_2020.6-2_amd64.deb Files: d7a6daf0fafe0ee4b26989e55e9037a0 20581692 science optional gromacs-data_2020.6-2_all.deb 1962e74b4ffe4ed5b2a4540043bd0ab1 821244 debug optional gromacs-dbgsym_2020.6-2_amd64.deb c89e38b6950ccadd5950da44347a4e95 85051644 debug optional gromacs-mpich-dbgsym_2020.6-2_amd64.deb c10276216fd8d5c211ff981ea90314bd 6863660 science optional gromacs-mpich_2020.6-2_amd64.deb 45e24b56e214da9decae4ce992b99a61 85056096 debug optional gromacs-openmpi-dbgsym_2020.6-2_amd64.deb 69a3120096c8b4e8f8a75f8c3b807c5d 6868232 science optional gromacs-openmpi_2020.6-2_amd64.deb d790eb5939b489598ae19b655c6bcb3d 15991 science optional gromacs_2020.6-2_amd64.buildinfo 8496a4d5dec5e62b2d623337032b1837 137236 science optional gromacs_2020.6-2_amd64.deb da8a4a83080448769044fa5ab2ac0132 187296 libdevel optional libgromacs-dev_2020.6-2_amd64.deb 44d7388f5311fde7d077081582da588b 121103916 debug optional libgromacs5-dbgsym_2020.6-2_amd64.deb 63983253290e5ee0f17bcfd917f6ba5f 11495956 libs optional libgromacs5_2020.6-2_amd64.deb Sun Jan 7 05:03:17 UTC 2024 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.C1oULqzK/gromacs_2020.6-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.C1oULqzK/gromacs_2020.6-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.C1oULqzK/gromacs_2020.6-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.C1oULqzK/b1/gromacs_2020.6-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.C1oULqzK/b2/gromacs_2020.6-2_amd64.changes ## close_archive (total time: 0.001s) 0.000s 12 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.deb.DebTarContainer 0.000s 4 calls diffoscope.comparators.deb.DebContainer 0.000s 8 calls diffoscope.comparators.tar.TarContainer ## command (total time: 13.831s) 6.075s 12 calls xz 4.785s 18 calls diff 0.948s 13 calls cmp 0.947s 13 calls cmp (external) 0.606s 3709 calls cmp (internal) 0.443s 11 calls js-beautify 0.028s 33 calls html2text ## compare_files (cumulative) (total time: 489.619s) 120.963s 1 call abc.DotChangesFile 120.062s 2 calls abc.DebFile 119.854s 4 calls abc.XzFile 113.044s 2 calls abc.DebDataTarFile 14.300s 1 call abc.JavaScriptFile 0.618s 2 calls abc.TarFile 0.509s 2 calls abc.Md5sumsFile 0.226s 3 calls abc.HtmlFile 0.043s 2 calls abc.TextFile ## container_extract (total time: 18.290s) 11.995s 32006 calls diffoscope.comparators.deb.DebTarContainer 6.076s 12 calls diffoscope.comparators.xz.XzContainer 0.128s 16 calls diffoscope.comparators.deb.DebContainer 0.091s 12 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 5.301s) 5.301s 16 calls linediff ## has_same_content_as (total time: 1.889s) 0.932s 3681 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.700s 10 calls abc.DebFile 0.233s 2 calls abc.DebDataTarFile 0.015s 4 calls abc.Md5sumsFile 0.006s 2 calls abc.TarFile 0.001s 6 calls abc.TextFile 0.001s 3 calls abc.HtmlFile 0.001s 4 calls abc.XzFile 0.000s 1 call abc.JavaScriptFile 0.000s 1 call abc.DotChangesFile ## main (total time: 147.424s) 147.262s 2 calls outputs 0.162s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 8 calls diffoscope.comparators.tar.TarContainer 0.000s 12 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.deb.DebTarContainer 0.000s 4 calls diffoscope.comparators.deb.DebContainer ## output (total time: 5.719s) 5.715s 1 call html 0.002s 1 call text 0.002s 1 call json ## recognizes (total time: 21.002s) 20.154s 12 calls diffoscope.comparators.binary.FilesystemFile 0.253s 1252 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.216s 14724 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.207s 512 calls diffoscope.comparators.utils.archive.ArchiveMember 0.172s 540 calls diffoscope.comparators.debian.DebControlMember 0.000s 32 calls abc.Md5sumsFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.873s) 0.873s 3714 calls specialize Sun Jan 7 05:05:45 UTC 2024 E: gromacs failed to build reproducibly in bullseye on amd64. Sun Jan 7 05:05:45 UTC 2024 E: diffoscope 240 found issues, please check https://tests.reproducible-builds.org/debian/dbd/bullseye/amd64/gromacs_2020.6-2.diffoscope.html Sun Jan 7 05:05:49 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Jan 7 05:05:49 UTC 2024 I: Submitting 20K b1/gromacs_2020.6-2_amd64.buildinfo.asc Sun Jan 7 05:05:51 UTC 2024 I: Submitting 20K b2/gromacs_2020.6-2_amd64.buildinfo.asc Sun Jan 7 05:05:53 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jan 7 05:05:53 UTC 2024 I: Done submitting .buildinfo files. Sun Jan 7 05:05:53 UTC 2024 I: Removing signed gromacs_2020.6-2_amd64.buildinfo.asc files: removed './b1/gromacs_2020.6-2_amd64.buildinfo.asc' removed './b2/gromacs_2020.6-2_amd64.buildinfo.asc'